Protein scaffolds for antibody mimics and other binding proteins

ABSTRACT

Disclosed herein are proteins that include an immunoglobulin fold and that can be used as scaffolds. Also disclosed herein are nucleic acids encoding such proteins and the use of such proteins in diagnostic methods and in methods for evolving novel compound-binding species and their ligands.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.11/543,316, filed Oct. 3, 2006, which is a divisional of U.S. patentapplication Ser. No. 10/728,078, filed Dec. 3, 2003 (now U.S. Pat. No.7,115,396), which is a continuation of U.S. patent application Ser. No.09/688,566, filed Oct. 16, 2000, which is a continuation-in-part of U.S.patent application Ser. No. 09/515,260, filed Feb. 29, 2000 (now U.S.Pat. No. 6,818,418), which is a continuation-in-part of U.S. patentapplication Ser. No. 09/456,693, filed Dec. 9, 1999, which claims thebenefit of U.S. Provisional Application No. 60/111,737, filed Dec. 10,1998. The contents of the aforementioned applications are herebyincorporated by reference.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted via EFS-Web and is hereby incorporated by reference in itsentirety. Said ASCII copy, created on Jun. 7, 2017, is namedMXI_517CP2DVCN_Sequence_Listing.txt and is 127,321 bytes in size.

BACKGROUND OF THE INVENTION

This invention relates to protein scaffolds useful, for example, for thegeneration of products having novel binding characteristics.

Proteins having relatively defined three-dimensional structures,commonly referred to as protein scaffolds, may be used as reagents forthe design of engineered products. These scaffolds typically contain oneor more regions which are amenable to specific or random sequencevariation, and such sequence randomization is often carried out toproduce libraries of proteins from which desired products may beselected. One particular area in which such scaffolds are useful is thefield of antibody design.

A number of previous approaches to the manipulation of the mammalianimmune system to obtain reagents or drugs have been attempted. Thesehave included injecting animals with antigens of interest to obtainmixtures of polyclonal antibodies reactive against specific antigens,production of monoclonal antibodies in hybridoma cell culture (Koehlerand Milstein, Nature 256:495, 1975), modification of existing monoclonalantibodies to obtain new or optimized recognition properties, creationof novel antibody fragments with desirable binding characteristics, andrandomization of single chain antibodies (created by connecting thevariable regions of the heavy and light chains of antibody moleculeswith a flexible peptide linker) followed by selection for antigenbinding by phage display (Clackson et al., Nature 352:624, 1991).

In addition, several non-immunoglobulin protein scaffolds have beenproposed for obtaining proteins with novel binding properties. Forexample, a “minibody” scaffold, which is related to the immunoglobulinfold, has been designed by deleting three beta strands from a heavychain variable domain of a monoclonal antibody (Tramontano et al., J.Mol. Recognit. 7:9, 1994). This protein includes 61 residues and can beused to present two hypervariable loops. These two loops have beenrandomized and products selected for antigen binding, but thus far theframework appears to have somewhat limited utility due to solubilityproblems. Another framework used to display loops has been tendamistat,a 74 residue, six-strand beta sheet sandwich held together by twodisulfide bonds (McConnell and Hoess, J. Mol. Biol. 250:460, 1995). Thisscaffold includes three loops, but, to date, only two of these loopshave been examined for randomization potential.

Other proteins have been tested as frameworks and have been used todisplay randomized residues on alpha helical surfaces (Nord et al., Nat.Biotechnol. 15:772, 1997; Nord et al., Protein Eng. 8:601, 1995), loopsbetween alpha helices in alpha helix bundles (Ku and Schultz, Proc.Natl. Acad. Sci. USA 92:6552, 1995), and loops constrained by disulfidebridges, such as those of the small protease inhibitors (Markland etal., Biochemistry 35:8045, 1996; Markland et al., Biochemistry 35:8058,1996; Rottgen and Collins, Gene 164:243, 1995; Wang et al., J. Biol.Chem. 270: 12250, 1995).

SUMMARY OF THE INVENTION

The present invention provides a new family of proteins capable ofevolving to bind any compound of interest. These proteins, whichgenerally make use of a scaffold derived from a fibronectin type III(Fn3) or Fn3-like domain, function in a manner characteristic of naturalor engineered antibodies (that is, polyclonal, monoclonal, orsingle-chain antibodies) and, in addition, possess structuraladvantages. Specifically, the structure of these antibody mimics hasbeen designed for optimal folding, stability, and solubility, even underconditions that normally lead to the loss of structure and function inantibodies.

These antibody mimics may be utilized for the purpose of designingproteins which are capable of binding to virtually any compound (forexample, any protein) of interest. ‘For example, the ¹⁰Fn3-basedmolecules described herein may be used as scaffolds which are subjectedto directed evolution to form a population with one or more randomizedFn3 loops that are analogous by position and structure to thecomplementarity-determining regions (CDRs) of an antibody variableregion, and/or to randomize Fn3's other three solvent exposed loops.Such a directed evolution approach results in the production ofantibody-like molecules with high affinities for antigens of interest.In addition, the scaffolds described herein may be used to displaydefined exposed loops (for example, loops previously randomized andselected on the basis of antigen binding) in order to direct theevolution of molecules that bind to such introduced loops. A selectionof this type may be carried out to identify recognition molecules forany individual CDR-like loop or, alternatively, for the recognition oftwo or all three CDR-like loops combined into a non-linear epitope.

Accordingly, in a first aspect, the present invention featuresrandomized or mutated scaffold proteins. In particular, the inventionfeatures a non-antibody protein including a domain having animmunoglobulin-like fold, the non-antibody protein deriving from areference protein by having a mutated amino acid sequence, wherein thenon-antibody protein binds with a Kd at least as tight as 1 μM to acompound that is not bound as tightly by the reference protein.

In addition, the invention features a non-antibody protein deriving froma scaffold protein including a domain having an immunoglobulin-likefold, wherein the amino acid sequence of the domain in the derivedprotein is more than 50% identical to the amino acid sequence of thedomain in the scaffold protein.

In yet another embodiment, the invention features a protein thatincludes a fibronectin type III domain having at least one randomizedloop, the protein being characterized by the ability of the Fn3 domainto bind to a compound that is not bound by the correspondingnaturally-occurring Fn3 domain.

In various preferred embodiments, any of these proteins of the inventionbind to their target compounds with a Kd at least as tight as 500 nM,preferably, with a Kd at least as tight as 100 nM or 10 nM, and, morepreferably, with a Kd at least as tight as 1 nM, 500 pM, 100 pM, or even20 pM. The protein preferably contains one, two, or three mutated loopsand at least one of the loops, and preferably two or all three of theloops, contributes to the binding of the protein to the compound.Additionally, the reference protein preferably lacks disulfide bonds,and the derivative protein may have at least one disulfide bond.

With respect to certain embodiments, the domain having animmunoglobulin-like fold preferably has a molecular mass less than 10 kDor greater than 7.5 kD, and, more preferably, has a molecular massbetween 7.5-10 kD. The proteins of the invention may be monomers underphysiological conditions or may be multimers, for example, dimers. Inother preferred embodiments, the reference protein used to derive amutated protein of the invention is a naturally-occurring mammalianprotein (for example, a human protein); and the domain having animmunoglobulin-like fold is mutated and includes up to 50%, andpreferably up to 34%, mutated amino acids as compared to theimmunoglobulin-like fold of the reference protein. In addition, thedomain having the immunoglobulin-like fold preferably consists ofapproximately 50-150 amino acids, and more preferably consists ofapproximately 50 amino acids.

Derivative proteins of the invention may be derived from any appropriatereference protein including, but not limited to, the preferred proteins,fibronectin or a fibronectin dimer, tenascin, N-cadherin, E-cadherin,ICAM, titin, GCSF-receptor, cytokine receptor, glycosidase inhibitor,antibiotic chromoprotein, myelin membrane adhesion molecule P0, CD8,CD4, CD2, class I MHC, T-cell antigen receptor, CD1, C2 and I-setdomains of VCAM-1, I-set immunoglobulin domain of myosin-binding proteinC, I-set immunoglobulin domain of myosin-binding protein H, I-setimmunoglobulin domain of telokin, NCAM, twitchin, neuroglian, growthhormone receptor, erythropoietin receptor, prolactin receptor,interferon-gamma receptor, β-galactosidase/glucuronidase,β-glucuronidase, transglutaminase, T-cell antigen receptor, superoxidedismutase, tissue factor domain, cytochrome F, green fluorescentprotein, GroEL, and thaumatin.

In further preferred embodiments of Fn3 domain-containing proteins, thefibronectin type III domain is a mammalian (for example, a human)fibronectin type III domain; and the protein includes the tenth moduleof the fibronectin type III (¹⁰Fn3) domain. In such proteins, compoundbinding is preferably mediated by either one, two, or three ¹⁰Fn3 loops.In other preferred embodiments, the second (DE) loop of ¹⁰Fn3 may beextended in length relative to the naturally-occurring module, or the¹⁰Fn3 may lack an integrin-binding motif. In these molecules, theintegrin-binding motif may be replaced by an amino acid sequence inwhich a polar amino acid-neutral amino acid-acidic amino acid sequence(in the N-terminal to C-terminal direction) replaces theintegrin-binding motif; alternatively, one preferred sequence isserine-glycine-glutamate. In another preferred embodiment, thefibronectin type III domain-containing proteins of the invention lackdisulfide bonds.

Any of the proteins of the invention (for example, the fibronectin typeIII domain-containing proteins) may be formulated as part of a fusionprotein. If the fusion protein is to be used for compound binding orcompound binding selections, the fusion protein includes a heterologousprotein that does not itself bind to the compound of interest. Theheterologous protein may, for example, be an antibody or antibody domain(such as an immunoglobulin F_(c) domain), a complement protein, a toxinprotein, or an albumin protein. In addition, any of the proteins of theinvention (for example, the fibronectin type III domain proteins) may becovalently bound to a nucleic acid (for example, an RNA), and thenucleic acid may encode the protein. Moreover, the protein may be amultimer, or, particularly if it lacks an integrin-binding motif, it maybe formulated in a physiologically-acceptable carrier.

The present invention also features proteins that include a fibronectintype III domain having at least one mutation in a β-sheet sequence.Again, these proteins are characterized by their ability to bind tocompounds that are not bound or are not bound as tightly by thecorresponding naturally-occurring fibronectin domain.

Any of the proteins of the invention may be immobilized on a solidsupport (for example, a bead or chip), and these proteins may bearranged in any configuration on the solid support, including an array.

In a related aspect, the invention further features nucleic acidsencoding any of the proteins of the invention. In preferred embodiments,the nucleic acid is DNA or RNA.

In another related aspect, the invention also features a method forgenerating a protein which includes a fibronectin type III domain andwhich is pharmaceutically acceptable to a mammal, involving removing theintegrin-binding domain of said fibronectin type III domain. This methodmay be applied to any of the fibronectin type III domain-containingproteins described above and is particularly useful for generatingproteins for human therapeutic applications. The invention also featuressuch fibronectin type III domain-containing proteins which lackintegrin-binding domains.

In yet another related aspect, the invention features methods ofobtaining derivative non-antibody proteins which bind to compounds ofinterest. One such method involves: (a) providing a non-antibodyscaffold protein including an immunoglobulin-like fold, wherein thescaffold protein does not bind to the compound with a Kd as tight as 1μM; (b) generating mutated derivatives of the non-antibody scaffoldprotein, thereby producing a library of mutated proteins; (c) contactingthe library with the compound; (d) selecting from the library at leastone derivative protein which binds to the compound with a Kd at least astight as 1 μM; and (e) optionally repeating steps (b)-(d) substitutingfor the non-antibody scaffold protein in repeated step (b) the productfrom the previous step (d). This technique may also be carried out withany of the proteins of the invention (for example, any of thefibronectin type III domain-containing proteins).

In yet other related aspects, the invention features screening methodswhich may be used to obtain or evolve randomized or mutated proteins ofthe invention capable of binding to compounds of interest, or to obtainor evolve compounds (for example, proteins) capable of binding to aparticular protein containing a randomized or mutated motif. Inaddition, the invention features screening procedures which combinethese two methods, in any order, to obtain either compounds or proteinsof interest.

In particular, a first screening method, useful for the isolation oridentification of randomized or mutated proteins of interest, involves:(a) contacting a compound of interest with a candidate protein, thecandidate protein being a derivative non-antibody protein including adomain having an immunoglobulin-like fold, the non-antibody proteinderiving from a reference protein by having a mutated amino acidsequence wherein the non-antibody protein binds with a Kd at least astight as 1 μM to a compound that is not bound as tightly by thereference protein, wherein the contacting is carried out underconditions that allow compound-protein complex formation; and (b)obtaining, from the complex, the derivative protein that binds to thecompound. This general technique may also be carried out with afibronectin type III domain protein having at least one randomized ormutated loop.

The second screening method is for isolating or identifying a compoundwhich binds to a protein of the invention. This method begins with anon-antibody protein including a domain having an immunoglobulin-likefold and deriving from a reference protein by having a mutated aminoacid sequence, wherein the non-antibody protein binds with a Kd at leastas tight as 1 μM to a compound that is not bound as tightly by thereference protein. This derivative protein is then contacted with acandidate compound, wherein the contacting is carried out underconditions that allow compound-protein complex formation, and thecompound which binds to the derivative protein is obtained from thecomplex. Again, this general technique may be carried out with anyprotein of the invention, for example, a protein with a mutatedfibronectin type III domain.

In addition, the invention features diagnostic methods which employ theproteins of the invention (for example, fibronectin type III scaffoldproteins and their derivatives). Such diagnostic methods may be carriedout on a sample (for example, a biological sample) to detect one analyteor to simultaneously detect many different analytes in the sample. Themethod may employ any of the scaffold molecules described herein.Preferably, the method involves (a) contacting the sample with a proteinof the invention that binds to the compound analyte, the contactingbeing carried out under conditions that allow compound-protein complexformation; and (b) detecting the complex, and therefore the compound inthe sample. In addition, this method may be used to quantitate, as wellas detect, compound levels in a sample.

In preferred embodiments of any of the selection or diagnostic methodsdescribed herein, the protein of the invention binds to its targetcompound with a Kd at least as tight as 1 μM or 500 nM, preferably, witha Kd at least as tight as 100 nM or 10 nM, and, more preferably, with aKd at least as tight as 1 nM, 500 pM, 100 pM, or even 20 pM. The proteinpreferably contains one, two, or three mutated loops and at least one ofthe loops, and preferably two or all three of the loops contributes tothe binding of the protein to the compound. Additionally, the referenceprotein preferably lacks disulfide bonds, and the derivative protein mayhave at least one disulfide bond.

With respect to certain embodiments of the methods, the domain having animmunoglobulin-like fold preferably has a molecular mass less than 10 kDor greater than 7.5 kD, and, more preferably, has a molecular massbetween 7.5-10 kD. The proteins of the invention may be monomers underphysiological conditions or may be multimers, for example, dimers. Inother preferred embodiments, the reference protein used to derive amutated protein of the invention is a naturally-occurring mammalianprotein (for example, a human protein); and the domain having animmunoglobulin-like fold is mutated and includes up to 50%, andpreferably up to 34%, mutated amino acids as compared to theimmunoglobulin-like fold of the reference protein. In addition, thedomain having an immunoglobulin-like fold preferably consists ofapproximately 50-150 amino acids, and more preferably consists ofapproximately 50 amino acids.

Derivative proteins used in the methods of the invention may be derivedfrom any appropriate reference protein including, but not limited to,the preferred proteins, fibronectin or a fibronectin dimer, tenascin,N-cadherin, E-cadherin, ICAM, titin, GCSF-receptor, cytokine receptor,glycosidase inhibitor, antibiotic chromoprotein, myelin membraneadhesion molecule P0, CD8, CD4, CD2, class I MHC, T-cell antigenreceptor, CD1, C2 and I-set domains of VCAM-1, I-set immunoglobulindomain of myosin-binding protein C, I-set immunoglobulin domain ofmyosin-binding protein H, I-set immunoglobulin domain of telokin, NCAM,twitchin, neuroglian, growth hormone receptor, erythropoietin receptor,prolactin receptor, interferon-gamma receptor,β-galactosidase/glucuronidase, β-glucuronidase, transglutaminase, T-cellantigen receptor, superoxide dismutase, tissue factor domain, cytochromeF, green fluorescent protein, GroEL, and thaumatin.

In addition, the steps of the selection methods described herein may berepeated with further mutation or randomization being carried outbetween cycles. For example, for the methods involving a protein havinga mutated or randomized fibronectin type III domain, at least one loopof the fibronectin type III domain of the protein obtained in step (b)may be mutated and steps (a) and (b) repeated using the furtherrandomized protein, or the compound obtained in step (b) may be modifiedand steps (a) and (b) repeated using the further modified compound. Inthese methods, the compound is preferably a protein, and the fibronectintype III domain is preferably a mammalian (for example, a human)fibronectin type III domain. In other preferred embodiments, the proteinincludes the tenth module of the fibronectin type III domain (¹⁰Fn3),and binding is mediated by one, two, or three ¹⁰Fn3 loops. In addition,the second (DE) loop of ¹⁰Fn3 may be extended in length relative to thenaturally-occurring module, or ¹⁰Fn3 may lack an integrin-binding motif.Again, as described above, the integrin-binding motif may be replaced byan amino acid sequence in which a basic amino acid-neutral aminoacid-acidic amino acid sequence (in the N-terminal to C-terminaldirection) replaces the integrin-binding motif; alternatively, onepreferred replacement sequence is serine-glycine-glutamate.

The selection and diagnostic methods described herein may be carried outusing any of the proteins of the invention (for example, a fibronectintype III domain-containing protein). In addition, any of these proteinsmay be formulated as part of a fusion protein with a heterologousprotein (for example, an antibody or antibody domain (including animmunoglobulin F_(c) domain) that does not itself bind the compound ofinterest, or a complement protein, toxin protein, or albumin protein).In addition, selections and diagnostic methods may be carried out usingthe proteins of the invention (for example, the fibronectin type IIIdomain proteins) covalently bound to nucleic acids (for example, RNAs orany nucleic acid which encodes the protein). Moreover, the selectionsand diagnostic methods may be carried out using these proteins (forexample, the fibronectin domain-containing proteins) as monomers or asmultimers, such as dimers.

Preferably, the selections and diagnostic methods involve theimmobilization of the binding target on a solid support. Preferred solidsupports include columns (for example, affinity columns, such asagarose-based affinity columns), microchips, or beads. Alternatively,the proteins (for example, the Fn3 domain-containing proteins) may beimmobilized and contacted with one or more potential binding targets.

For the diagnostic methods, the compound is often a protein, but mayalso be any other analyte in a sample. Detection may be accomplished byany standard technique including, without limitation, radiography,fluorescence detection, mass spectroscopy, or surface plasmon resonance.

In a final aspect, the invention features a non-antibody protein thatbinds tumor necrosis factor-α (TNF-α) with a Kd at least as tight as 1μM, the protein having a sequence that is less than 20% identical toTNF-α receptor (for example, a naturally-occurring TNF-α receptor, suchas a mammalian or human TNF-α receptor).

In preferred embodiments, this protein includes a mutated fibronectintype III domain and the protein is mutated in the DE, BC, and FG loops.Preferably, the mutated FG loop is the same length as the wild-type FGloop. In other preferred embodiments, the protein includes animmunoglobulin-like fold (preferably, having a molecular mass less than10 kD, greater than 7.5 kD, or between 7.5-10 kD) that consists ofapproximately 50-150 amino acids, and preferably, approximately 50 aminoacids.

The TNF-α binders according to the invention bind TNF-α with a Kd atleast as tight as 1 μM, preferably, at least as tight as 500 nM, 100 nM,or 10 nM, more preferably, at least as tight as 1 nM or 500 pM, and,most preferably, at least as tight as 100 pM or even 20 pM. Preferably,these proteins contain one, two, or three mutated loops, and at leastone, and preferably two or all three of the loops, contribute to thebinding of the non-antibody protein to TNF-α. In other preferredembodiments, the non-antibody protein has at least one disulfide bond,and the non-antibody protein is a monomer or dimer under physiologicalconditions.

The TNF-α binders may be immobilized on a solid support (for example, achip or bead), and may be part of an array. In addition, any of theTNF-α binders may be joined to a heterologous protein (for example, aheterologous protein that is an antibody or an antibody domain that doesnot bind TNF-α, an immunoglobulin F_(c) domain, a complement protein, oran albumin protein).

If desired, the protein may include a mutated fibronectin type IIIdomain (for example, one derived from a human fibronectin type IIIdomain, such as a mutated tenth module of the fibronectin type IIIdomain (¹⁰Fn3)). In addition, the protein may lack an ¹⁰Fn3integrin-binding motif. TNF-α binders preferably include a non-naturallyoccurring sequence in a loop of ¹⁰Fn3 (for example, the loop sequencePW(A/G), and may include a non-naturally occurring sequence in a β-sheetof ¹⁰Fn3. Particularly preferred TNF-α binders of the invention areshown in FIG. 25 (SEQ ID NOS: 34-140).

In addition, in related aspects, the invention features nucleic acidsencoding any of the TNF-α binding proteins of the invention, as well asa loop structure on any protein that includes any one of the amino acidsequences of FIG. 25 (SEQ ID NOS: 34-140).

As used herein, by “non-antibody protein” is meant a protein that is notproduced by the B cells of a mammal either naturally or followingimmunization of a mammal. This term also excludes antibody fragments ofmore than 100 amino acids, preferably, more than 80 amino acids, and,most preferably, more than 50 amino acids in length.

By “immunoglobulin-like fold” is meant a protein domain of between about80-150 amino acid residues that includes two layers of antiparallelbeta-sheets, and in which the flat, hydrophobic faces of the twobeta-sheets are packed against each other. Proteins according to theinvention may include several immunoglobulin-like folds covalently boundor associated non-covalently into larger structures.

By “scaffold” is meant a protein used to select or design a proteinframework with specific and favorable properties, such as binding. Whendesigning proteins from the scaffold, amino acid residues that areimportant for the framework's favorable properties are retained, whileothers residues may be varied. Such a scaffold has less than 50% of theamino acid residues that vary between protein derivatives havingdifferent properties and greater than or equal to 50% of the residuesthat are constant between such derivatives. Most commonly, theseconstant residues confer the same overall three-dimensional fold to allthe variant domains, regardless of their properties.

By “fibronectin type III domain” is meant a domain having 7 or 8 betastrands which are distributed between two beta sheets, which themselvespack against each other to form the core of the protein, and furthercontaining loops which connect the beta strands to each other and aresolvent exposed. There are at least three such loops at each edge of thebeta sheet sandwich, where the edge is the boundary of the proteinperpendicular to the direction of the beta strands. Preferably, afibronectin type III domain includes a sequence which exhibits at least30% amino acid identity, and preferably at least 50% amino acididentity, to the sequence encoding the structure of the ¹⁰Fn3 domainreferred to as “1ttg” (ID=“1ttg” (one ttg)) available from the RCSB(Research Collaboratory for Structural Bioinformatics) Protein DataBase. Sequence identity referred to in this definition is determined bythe Homology program, available from Molecular Simulation (San Diego,Calif.). The invention further includes polymers of ¹⁰Fn3-relatedmolecules, which are an extension of the use of the monomer structure,whether or not the subunits of the polyprotein are identical.

By “naturally occurring” is meant any protein that is encoded by aliving organism.

By “randomized” or “mutated” is meant including one or more amino acidalterations relative to a template sequence. By “randomizing” or“mutating” is meant the process of introducing, into a sequence, such anamino acid alteration. Randomization or mutation may be accomplishedthrough intentional, blind, or spontaneous sequence variation, generallyof a nucleic acid coding sequence, and may occur by any technique, forexample, PCR, error-prone PCR, or chemical DNA synthesis. By a“corresponding, non-mutated protein” is meant a protein that isidentical in sequence, except for the introduced amino acid mutations.

By a “protein” is meant any sequence of two or more amino acids,regardless of length, post-translation modification, or function.“Protein” and “peptide” are used interchangeably herein.

By “RNA” is meant a sequence of two or more covalently bonded, naturallyoccurring or modified ribonucleotides. One example of a modified RNAincluded within this term is phosphorothioate RNA.

By “DNA” is meant a sequence of two or more covalently bonded, naturallyoccurring or modified deoxyribonucleotides.

By a “nucleic acid” is meant any two or more covalently bondednucleotides or nucleotide analogs or derivatives. As used herein, thisterm includes, without limitation, DNA, RNA, and PNA.

By “pharmaceutically acceptable” is meant a compound or protein that maybe administered to an animal (for example, a mammal) without significantadverse medical consequences.

By “physiologically acceptable carrier” is meant a carrier which doesnot have a significant detrimental impact on the treated host and whichretains the therapeutic properties of the compound with which it isadministered. One exemplary physiologically acceptable carrier isphysiological saline. Other physiologically acceptable carriers andtheir formulations are known to one skilled in the art and aredescribed, for example, in Remington's Pharmaceutical Sciences, (18^(th)edition), ed. A. Gennaro, 1990, Mack Publishing Company, Easton, Pa.,incorporated herein by reference.

By a “fusion protein” is meant a protein that includes (i) a scaffoldprotein of the invention joined to (ii) a second, different (i.e.,“heterologous”) protein. “Fusion proteins” are distinguished from“nucleic acid-protein fusions” and “RNA-protein fusions” in that a“fusion protein” is composed entirely of amino acids, while both a“nucleic acid-protein fusion” and an “RNA-protein fusion” include astretch of nucleic acids (the nucleic acid or RNA component) joined to astretch of amino acids (the protein component).

By “selecting” is meant substantially partitioning a molecule from othermolecules in a population. As used herein, a “selecting” step providesat least a 2-fold, preferably, at least a 30-fold, more preferably, atleast a 100-fold, and, most preferably, at least a 1000-fold enrichmentof a desired molecule relative to undesired molecules in a populationfollowing the selection step. A selection step may be repeated anynumber of times, and different types of selection steps may be combinedin a given approach.

By “binding partner,” as used herein, is meant any molecule which has aspecific, covalent or non-covalent affinity for a portion of a desiredcompound (for example, protein) of interest. Examples of bindingpartners include, without limitation, members of antigen/antibody pairs,protein/inhibitor pairs, receptor/ligand pairs (for example cell surfacereceptor/ligand pairs, such as hormone receptor/peptide hormone pairs),enzyme/substrate pairs (for example, kinase/substrate pairs),lectin/carbohydrate pairs, oligomeric or heterooligomeric proteinaggregates, DNA binding protein/DNA binding site pairs, RNA/proteinpairs, and nucleic acid duplexes, heteroduplexes, or ligated strands, aswell as any molecule which is capable of forming one or more covalent ornon-covalent bonds (for example, disulfide bonds) with any portion ofanother molecule (for example, a compound or protein).

By a “solid support” is meant, without limitation, any column (or columnmaterial), bead, test tube, microtiter dish, solid particle (forexample, agarose or sepharose), microchip (for example, silicon,silicon-glass, or gold chip), or membrane (for example, an inorganicmembrane, nitrocellulose, or the membrane of a liposome or vesicle) towhich an antibody mimic or an affinity complex may be bound, eitherdirectly or indirectly (for example, through other binding partnerintermediates such as other antibodies or Protein A), or in which anantibody mimic or an affinity complex may be embedded (for example,through a receptor or channel).

The present invention provides a number of advantages. For example, asdescribed in more detail below, the present antibody mimics exhibitimproved biophysical properties, such as stability under reducingconditions and solubility at high concentrations. In addition, thesemolecules may be readily expressed and folded in prokaryotic systems,such as E. coli, in eukaryotic systems, such as yeast, and in in vitrotranslation systems, such as the rabbit reticulocyte lysate system.Moreover, these molecules are extremely amenable to affinity maturationtechniques involving multiple cycles of selection, including in vitroselection using RNA-protein fusion technology (Roberts and Szostak,Proc. Natl. Acad. Sci USA 94:12297, 1997; Szostak et al., U.S. Ser. No.09/007,005 and U.S. Ser. No. 09/247,190; Szostak et al. WO98/31700),phage display (see, for example, Smith and Petrenko, Chem. Rev. 97:317,1997), and yeast display systems (see, for example, Boder and Wittrup,Nature Biotech. 15:553, 1997).

Other features and advantages of the present invention will be apparentfrom the following detailed description thereof, and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a photograph showing a comparison between the structures ofantibody heavy chain variable regions from camel (dark blue) and llama(light blue), in each of two orientations.

FIG. 2 is a photograph showing a comparison between the structures ofthe camel antibody heavy chain variable region (dark blue), the llamaantibody heavy chain variable region (light blue), and a fibronectintype III module number 10 (¹⁰Fn3) (yellow).

FIG. 3 is a photograph showing a fibronectin type III module number 10(¹⁰Fn3), with the loops corresponding to the antigen-binding loops inIgG heavy chains highlighted in red.

FIG. 4 is a graph illustrating a sequence alignment between afibronectin type III protein domain and related protein domains.

FIG. 5 is a photograph showing the structural similarities between a¹⁰Fn3 domain and 15 related proteins, including fibronectins, tenascins,collagens, and undulin. In this photograph, the regions are labeled asfollows: constant, dark blue; conserved, light blue; neutral, white;variable, red; and RGD integrin-binding motif (variable), yellow.

FIG. 6 is a photograph showing space filling models of fibronectin IIImodules 9 and 10, in each of two different orientations. The two modulesand the integrin binding loop (RGD) are labeled. In this figure, blueindicates positively charged residues, red indicates negatively chargedresidues, and white indicates uncharged residues.

FIG. 7 is a photograph showing space filling models of fibronectin IIImodules 7-10, in each of three different orientations. The four modulesare labeled. In this figure, blue indicates positively charged residues,red indicates negatively charged residues, and white indicates unchargedresidues.

FIG. 8 is a photograph illustrating the formation, under different saltconditions, of RNA-protein fusions which include fibronectin type IIIdomains.

FIG. 9 is a series of photographs illustrating the selection offibronectin type III domain-containing RNA-protein fusions, as measuredby PCR signal analysis.

FIG. 10 is a graph illustrating an increase in the percent TNF-α bindingduring the selections described herein, as well as a comparison betweenRNA-protein fusion and free protein selections.

FIG. 11 is a series of schematic representations showing IgG, ¹⁰Fn3,Fn-CH₁, —CH₂—CH₃, and Fn-CH₂—CH₃ (clockwise from top left).

FIG. 12 is a photograph showing a molecular model of Fn-CH₁, —CH₂— CH₃based on known three-dimensional structures of IgG (X-raycrystallography) and ¹⁰Fn3 (NMR and X-ray crystallography).

FIG. 13 is a graph showing the time course of an exemplary ¹⁰Fn3-basednucleic acid-protein fusion selection of TNF-α binders. The proportionof nucleic acid-protein fusion pool (open diamonds) and free proteinpool (open circles) that bound to TNF-α-Sepharose, and the proportion offree protein pool (full circles) that bound to underivatized Sepharose,are shown.

FIGS. 14 and 15 are graphs illustrating TNF-α binding by TNF-αFn-binders. In particular, these figures show mass spectra data obtainedfrom a ¹⁰Fn3 fusion chip and non-fusion chip, respectively.

FIGS. 16 and 17 are the phosphorimage and fluorescence scan,respectively, of an ¹⁰Fn3 array, illustrating TNF-α binding.

FIG. 18 is a graph showing an alignment of the primary sequences of thellama V_(H) domain and the wild-type human ¹⁰Fn3 domain. Homologousresidues between the two sequences are indicated. The ¹⁰Fn3 residuesoutside the randomized loops that were found to have mutated inapproximately 45% of the selected clones are marked with arrows underthe wild-type ¹⁰Fn3 sequence and with the letter that identifies theselected residue.

FIG. 19 shows schematic representations of the llama V_(H) domain andthe wild-type human ¹⁰Fn3 domain. The locations of the mutated frameworkresidues are indicated.

FIG. 20 is a graph illustrating the efficiency and specificity ofbinding of a free-protein pool translated from the original library (R0)and after ten rounds of selection with TNF-α (R10). Protein pool bindingto underivatized Sepharose, to TNF-α-Sepharose, to IL-1α-Sepharose, andto IL-13-Sepharose is compared.

FIG. 21 is a series of IgG-like scaffolds for the display of up to threeloops.

FIG. 22 is a series of IgG-like scaffolds for the display of up to four,or even six, loops.

FIG. 23 is a series of scaffolds, unrelated to IgG, for the display ofloop structures.

FIGS. 24A-24D are photographic and graphic illustrations demonstratingthe specific capture of a target (TNF-α) by a mimic immobilized on asolid surface.

FIGS. 25A-25D are graphs listing exemplary TNF-α binders (SEQ ID NOS:33-140) according to the invention.

DETAILED DESCRIPTION

The novel antibody mimics described herein have been designed to besuperior both to antibody-derived fragments and to non-antibodyframeworks, for example, those frameworks cited above.

The major advantage of these antibody mimics over antibody fragments isstructural. These antibody mimics are derived from whole, stable, andsoluble structural scaffolds. For example, the Fn3 scaffold is found inthe human body. Consequently, they exhibit better folding andthermostability properties than antibody fragments, whose creationinvolves the removal of parts of the antibody native fold, oftenexposing amino acid residues that, in an intact antibody, would beburied in a hydrophobic environment, such as an interface betweenvariable and constant domains. Exposure of such hydrophobic residues tosolvent increases the likelihood of aggregation of the antibodyfragments.

In addition, the scaffolds described herein have no disulfide bonds,which have been reported to retard or prevent proper folding of antibodyfragments under certain conditions. Since the present scaffolds do notrely on disulfides for native fold stability, they are stable underreducing conditions, unlike antibodies and their fragments which unravelupon disulfide bond reduction.

Moreover, these scaffolds provide the functional advantages of antibodymolecules. In particular, despite the fact that the ¹⁰Fn3 module is notan immunoglobulin, its overall fold is close to that of the variableregion of the IgG heavy chain (FIG. 2), making it possible to displaythe three fibronectin loops analogous to CDRs in relative orientationssimilar to those of native antibodies. Because of this structure, thepresent antibody mimics possess antigen binding properties that aresimilar in nature and affinity to those of antibodies, and a looprandomization and shuffling strategy may be employed in vitro that issimilar to the process of affinity maturation of antibodies in vivo.

There are now described below exemplary scaffolds, for example,fibronectin-based scaffolds, and their use for identifying, selecting,and evolving novel binding proteins as well as their target ligands.These examples are provided for the purpose of illustrating, and notlimiting, the invention.

¹⁰Fn3 Structural Motif

Preferred antibody mimics of the present invention are based on thestructure of a fibronectin module of type III (Fn3), a common domainfound in mammalian blood and structural proteins. This domain occursmore than 400 times in the protein sequence database and has beenestimated to occur in 2% of the proteins sequenced to date, includingfibronectins, tenascin, intracellular cytoskeletal proteins, andprokaryotic enzymes (Bork and Doolittle, Proc. Natl. Acad. Sci. USA89:8990, 1992; Bork et al., Nature Biotech. 15:553, 1997; Meinke et al.,J. Bacteriol. 175:1910, 1993; Watanabe et al., J. Biol. Chem. 265:15659,1990). A particular scaffold is the tenth module of human Fn3 (¹⁰Fn3),which comprises 94 amino acid residues. The overall fold of this domainis closely related to that of the smallest functional antibody fragment,the variable region of the heavy chain, which comprises the entireantigen recognition unit in camel and llama IgG (FIG. 1, 2). The majordifferences between camel and llama domains and the ¹⁰Fn3 domain arethat (i)¹⁰Fn3 has fewer beta strands (seven vs. nine) and (ii) the twobeta sheets packed against each other are connected by a disulfidebridge in the camel and llama domains, but not in ¹⁰Fn3.

The three loops of ¹⁰Fn3 corresponding to the antigen-binding loops ofthe IgG heavy chain run between amino acid residues 21-31 (BC), 51-56(DE), and 76-88 (FG) (FIG. 3). The length of the BC and DE loop, 10 and6 residues, respectively, fall within the narrow range of thecorresponding antigen-recognition loops found in antibody heavy chains,that is, 7-10 and 4-8 residues, respectively. Accordingly, oncerandomized and selected for high antigen affinity, these two loops maymake contacts with antigens equivalent to the contacts of thecorresponding loops in antibodies.

In contrast, the FG loop of ¹⁰Fn3 is 12 residues long, whereas thecorresponding loop in antibody heavy chains ranges from 4-28 residues.To optimize antigen binding, therefore, the length of the FG loop of¹⁰Fn3 is preferably randomized in length as well as in sequence to coverthe CDR3 range of 4-28 residues to obtain the greatest possibleflexibility and affinity in antigen binding. Indeed, in general, thelengths as well as the sequences of the CDR-like loops of the antibodymimics may be randomized during in vitro or in vivo affinity maturation(as described in more detail below).

The tenth human fibronectin type III domain, ¹⁰Fn3, refolds rapidly evenat low temperature; its backbone conformation has been recovered within1 second at 5° C. Thermodynamic stability of ¹⁰Fn3 is high (ΔGu=24kJ/mol=5.7 kcal/mol), correlating with its high melting temperature of110° C.

One of the physiological roles of ¹⁰Fn3 is as a subunit of fibronectin,a glycoprotein that exists in a soluble form in body fluids and in aninsoluble form in the extracellular matrix (Dickinson et al., J. Mol.Biol. 236:1079, 1994). A fibronectin monomer of 220-250 kD contains 12type I modules, two type II modules, and 17 fibronectin type III modules(Potts and Campbell, Curr. Opin. Cell Biol. 6:648, 1994). Different typeIII modules are involved in the binding of fibronectin to integrins,heparin, and chondroitin sulfate. ¹⁰Fn3 was found to mediate celladhesion through an integrin-binding Arg-Gly-Asp (RGD) motif on one ofits exposed loops. Similar RGD motifs have been shown to be involved inintegrin binding by other proteins, such as fibrinogen, von Wellebrandfactor, and vitronectin (Hynes et al., Cell 69:11, 1992). No othermatrix- or cell-binding roles have been described for ¹⁰Fn3.

The observation that ¹⁰Fn3 has only slightly more adhesive activity thana short peptide containing RGD is consistent with the conclusion thatthe cell-binding activity of ¹⁰Fn3 is localized in the RGD peptiderather than distributed throughout the ¹⁰Fn3 structure (Baron et al.,Biochemistry 31:2068, 1992). The fact that ¹⁰Fn3 without the RGD motifis unlikely to bind to other plasma proteins or extracellular matrixmakes ¹⁰Fn3 a useful scaffold to replace antibodies. In addition, thepresence of ¹⁰Fn3 in natural fibrinogen in the bloodstream suggests that¹⁰Fn3 itself is unlikely to be immunogenic in the organism of origin.

In addition, we have determined that the ¹⁰Fn3 framework possessesexposed loop sequences tolerant of randomization, facilitating thegeneration of diverse pools of antibody mimics. This determination wasmade by examining the flexibility of the ¹⁰Fn3 sequence. In particular,the human ¹⁰Fn3 sequence was aligned with the sequences of fibronectinsfrom other sources as well as sequences of related proteins (FIG. 4),and the results of this alignment were mapped onto the three-dimensionalstructure of the human ¹⁰Fn3 domain (FIG. 5). This alignment revealedthat the majority of conserved residues are found in the core of thebeta sheet sandwich, whereas the highly variable residues are 5 locatedalong the edges of the beta sheets, including the N- and C-termini, onthe solvent-accessible faces of both beta sheets, and on threesolvent-accessible loops that serve as the hypervariable loops foraffinity maturation of the antibody mimics. In view of these results,the randomization of these three loops are unlikely to have an adverseeffect on the overall fold or stability of the ¹⁰Fn3 framework itself.

For the human ¹⁰Fn3 sequence, this analysis indicates that, at aminimum, amino acids 1-9, 44-50, 61-54, 82-94 (edges of beta sheets);19, 21, 30-46 (even), 79-65 (odd) (solvent-accessible faces of both betasheets); 21-31, 51-56, 76-88 (CDR-like solvent-accessible loops); and14-16 and 36-45 (other solvent-accessible loops and beta turns) may berandomized to evolve new or improved compound-binding proteins. Inaddition, as discussed above, alterations in the lengths of one or moresolvent exposed loops may also be included in such directed evolutionmethods.

Alternatively, changes in the β-sheet sequences may also be used toevolve new proteins. These mutations change the scaffold and therebyindirectly alter loop structure(s). If this approach is taken, mutationsshould not saturate the sequence, but rather few mutations should beintroduced. Preferably, no more than between 3-20 changes should beintroduced to the (3-sheet sequences by this approach.

Sequence variation may be introduced by any technique including, forexample, mutagenesis by Taq polymerase (Tindall and Kunkel, Biochemistry27:6008 (1988)), fragment recombination, or a combination thereof.Similarly, an increase of the structural diversity of libraries, forexample, by varying the length as well as the sequence of the CDR-likeloops, or by structural redesign based on the advantageous frameworkmutations found in selected pools, may be used to introduce furtherimprovements in antibody mimic scaffolds.

Antibody Mimic Fusions

The antibody mimics described herein may be fused to other proteindomains. For example, these mimics may be integrated with the humanimmune response by fusing the constant region of an IgG (F_(c)) with anantibody mimic, such as an ¹⁰Fn3 module, preferably through theC-terminus of ¹⁰Fn3. The F_(c) in such a ¹⁰Fn3-F_(c) fusion moleculeactivates the complement component of the immune response and increasesthe therapeutic value of the antibody mimic. Similarly, a fusion betweenan antibody mimic, such as ¹⁰Fn3, and a complement protein, such as C1q,may be used to target cells, and a fusion between an antibody mimic,such as ¹⁰Fn3, and a toxin may be used to specifically destroy cellsthat carry a particular antigen. In addition, an antibody scaffold, suchas ¹⁰Fn3, in any form may be fused with albumin to increase itshalf-life in the bloodstream and its tissue penetration. Any of thesefusions may be generated by standard techniques, for example, byexpression of the fusion protein from a recombinant fusion geneconstructed using publically available gene sequences.

Scaffold Multimers

In addition to monomers, any of the scaffold constructs described hereinmay be generated as dimers or multimers of antibody mimics as a means toincrease the valency and thus the avidity of antigen binding. Suchmultimers may be generated through covalent binding. For example,individual ¹⁰Fn3 modules may be bound by imitating the natural⁸Fn3-⁹Fn3-¹⁰Fn3 C-to-N-terminus binding or by imitating antibody dimersthat are held together through their constant regions. A ¹⁰Fn3-Fcconstruct may be exploited to design dimers of the general scheme of¹⁰Fn3-Fc::Fc-¹⁰Fn3. The bonds engineered into the Fc::Fc interface maybe covalent or non-covalent. In addition, dimerizing or multimerizingpartners other than Fc can be used in hybrids, such as ¹⁰Fn3 hybrids, tocreate such higher order structures.

In particular examples, covalently bonded multimers may be generated byconstructing fusion genes that encode the multimer or, alternatively, byengineering codons for cysteine residues into monomer sequences andallowing disulfide bond formation to occur between the expressionproducts. Non-covalently bonded multimers may also be generated by avariety of techniques. These include the introduction, into monomersequences, of codons corresponding to positively and/or negativelycharged residues and allowing interactions between these residues in theexpression products (and therefore between the monomers) to occur. Thisapproach may be simplified by taking advantage of charged residuesnaturally present in a monomer subunit, for example, the negativelycharged residues of fibronectin. Another means for generatingnon-covalently bonded antibody mimics is to introduce, into the monomergene (for example, at the amino- or carboxy-termini), the codingsequences for proteins or protein domains known to interact. Suchproteins or protein domains include coil-coil motifs, leucine zippermotifs, and any of the numerous protein subunits (or fragments thereof)known to direct formation of dimers or higher order multimers.

Fibronectin-Like Molecules

Although ¹⁰Fn3 represents a preferred scaffold for the generation ofantibody mimics, other molecules may be substituted for ¹⁰Fn3 in themolecules described herein. These include, without limitation, humanfibronectin modules ¹Fn3-⁹Fn3 and ¹¹Fn3-¹⁷Fn3 as well as related Fn3modules from non-human animals and prokaryotes. In addition, Fn3 modulesfrom other proteins with sequence homology to ¹⁰Fn3, such as tenascinsand undulins, may also be used. Other exemplary scaffolds havingimmunoglobulin-like folds (but with sequences that are unrelated to theV_(H) domain) are shown in FIG. 21 and include N-cadherin, ICAM-2,titin, GCSF receptor, cytokine receptor, glycosidase inhibitor,E-cadherin, and antibiotic chromoprotein. Yet further domains withrelated structures may be derived from myelin membrane adhesion moleculeP0, CD8, CD4, CD2, class I MHC, T-cell antigen receptor, CD1, C2 andI-set domains of VCAM-1, I-set immunoglobulin domain of myosin-bindingprotein C, I-set immunoglobulin domain of myosin-binding protein H,I-set immunoglobulin domain of telokin, telikin, NCAM, twitchin,neuroglian, growth hormone receptor, erythropoietin receptor, prolactinreceptor, GC-SF receptor, interferon-gamma receptor,β-galactosidase/glucuronidase, β-glucuronidase, and transglutaminase.Alternatively, any other protein that includes one or moreimmunoglobulin-like folds may be utilized. Such proteins may beidentified, for example, using the program SCOP (Murzin et al., J. Mol.Biol. 247:536 (1995); Lo Conte et al., Nucleic Acids Res. 25:257 (2000).

Generally, any molecule that exhibits a structural relatedness to theV_(H) domain (as identified, for example, using the computer programabove) may be utilized as an antibody mimic. Such molecules may, likefibronectin, include three loops at the N-terminal pole of the moleculeand three loops at the C-terminal pole, each of which may be randomizedto create diverse libraries; alternatively, larger domains may beutilized, having larger numbers of loops, as long as a number of suchsurface randomizable loops are positioned closely enough in space thatthey can participate in antigen binding. FIG. 22 shows examples ofuseful domains having more than three loops positioned close to eachother. These examples include T-cell antigen receptor and superoxidedismutase, which each have four loops that can be randomized; and an Fn3dimer, tissue factor domains, and cytokine receptor domains, each ofwhich have three sets of two similar domains where three randomizableloops are part of the two domains (bringing the total number of loops tosix).

In yet another alternative, any protein having variable loops positionedclose enough in space may be utilized for candidate binding proteinproduction. For example, large proteins having spatially related,solvent accessible loops may be used, even if unrelated structurally toan immunoglobulin-like fold. Exemplary proteins include, withoutlimitation, cytochrome F, green fluorescent protein, GroEL, andthaumatin (FIG. 23). The loops displayed by these proteins may berandomized and superior binders selected from a randomized library asdescribed herein. Because of their size, molecules may be obtained thatexhibit an antigen binding surface considerably larger than that foundin an antibody-antigen interaction. Other useful scaffolds of this typemay also be identified using the program SCOP (Murzin et al., J. Mol.Biol. 247:536 (1995)) to browse among candidate proteins having numerousloops, particularly loops positioned among parallel beta sheets or anumber of alpha-helices.

Modules from different organisms and parent proteins may be mostappropriate for different applications. For example, in designing anantibody mimic, it may be most desirable to generate that protein from afibronectin or fibronectin-like molecule native to the organism forwhich a therapeutic is intended. In contrast, the organism of origin isless important or even irrelevant for antibody mimics that are to beused for in vitro applications, such as diagnostics, or as researchreagents.

For any of these molecules, libraries may be generated and used toselect binding proteins by any of the methods described herein.

Directed Evolution of Scaffold-Based Binding Proteins

The antibody mimics described herein may be used in any technique forevolving new or improved binding proteins. In one particular example,the target of binding is immobilized on a solid support, such as acolumn resin or microtiter plate well, and the target contacted with alibrary of candidate scaffold-based binding proteins. Such a library mayconsist of antibody mimic clones, such as 10Fn3 clones constructed fromthe wild type ¹⁰Fn3 scaffold through randomization of the sequenceand/or the length of the ¹⁰Fn3 CDR-like loops. If desired, this librarymay be an RNA-protein fusion library generated, for example, by thetechniques described in Szostak et al., U.S. Ser. Nos. 09/007,005 and09/247,190; Szostak et al., WO98/31700; and Roberts & Szostak, Proc.Natl. Acad. Sci. USA (1997) vol. 94, p. 12297-12302. Alternatively, itmay be a DNA-protein library (for example, as described in Lohse,DNA-Protein Fusions and Uses Thereof, U.S. Ser. No. 60/110,549, U.S.Ser. No. 09/459,190, and WO 00/32823). The fusion library is incubatedwith the immobilized target, the support is washed to removenon-specific binders, and the tightest binders are eluted under verystringent conditions and subjected to PCR to recover the sequenceinformation or to create a new library of binders which may be used torepeat the selection process, with or without further mutagenesis of thesequence. A number of rounds of selection may be performed until bindersof sufficient affinity for the antigen are obtained.

In one particular example, the ¹⁰Fn3 scaffold may be used as theselection target. For example, if a protein is required that binds aspecific peptide sequence presented in a ten residue loop, a single¹⁰Fn3 clone is constructed in which one of its loops has been set to thelength often and to the desired sequence. The new clone is expressed invivo and purified, and then immobilized on a solid support. AnRNA-protein fusion library based on an appropriate scaffold is thenallowed to interact with the support, which is then washed, and desiredmolecules eluted and re-selected as described above.

Similarly, the scaffolds described herein, for example, the ¹⁰Fn3scaffold, may be used to find natural proteins that interact with thepeptide sequence displayed by the scaffold, for example, in an ¹⁰Fn3loop. The scaffold protein, such as the ¹⁰Fn3 protein, is immobilized asdescribed above, and an RNA-protein fusion library is screened forbinders to the displayed loop. The binders are enriched through multiplerounds of selection and identified by DNA sequencing.

In addition, in the above approaches, although RNA-protein librariesrepresent exemplary libraries for directed evolution, any type ofscaffold-based library may be used in the selection methods of theinvention.

Use

The antibody mimics described herein may be evolved to bind any antigenof interest. These proteins have thermodynamic properties superior tothose of natural antibodies and can be evolved rapidly in vitro.Accordingly, these antibody mimics may be employed in place ofantibodies in all areas in which antibodies are used, including in theresearch, therapeutic, and diagnostic fields. In addition, because thesescaffolds possess solubility and stability properties superior toantibodies, the antibody mimics described herein may also be used underconditions which would destroy or inactivate antibody molecules.Finally, because the scaffolds of the present invention may be evolvedto bind virtually any compound, these molecules provide completely novelbinding proteins which also find use in the research, diagnostic, andtherapeutic areas.

Experimental Results

Exemplary scaffold molecules described above were generated and tested,for example, in selection protocols, as follows.

Library Construction

A complex library was constructed from three fragments, each of whichcontained one randomized area corresponding to a CDR-like loop. Therandomized residues are indicated in FIG. 18 as underlined sequences,specifically, residues 23-29 of the ¹⁰Fn3 BC loop (corresponding toCDR-H1 of the llama V_(H)); residues 52-55 of the ¹⁰Fn3 DE loop(corresponding to CDR-H2 of the llama V_(H)); and residues 78-87 of the¹⁰Fn3 FG loop (corresponding to CDR-H3 of the llama V_(H)). Thefragments were named BC, DE, and FG based on the names of the CDR-H-likeloops contained within them; in addition to ¹⁰Fn3 and a randomizedsequence, each of the fragments contained stretches encoding anN-terminal His₆ domain or a C-terminal FLAG peptide tag. At eachjunction between two fragments (i.e., between the BC and DE fragments orbetween the DE and FG fragments), each DNA fragment containedrecognition sequences for the Earl Type IIS restriction endonuclease.This restriction enzyme allowed the splicing together of adjacentfragments while removing all foreign, non-¹⁰Fn3, sequences. It alsoallowed for a recombination-like mixing of the three ¹⁰Fn3 fragmentsbetween cycles of mutagenesis and selection.

The wild-type, human ¹⁰Fn3 gene was cloned from a human liver library(Maxim Biotech, South San Francisco, Calif.) using the primersHu5PCR-Ndel 5′CATATGGTTTCTGATGTTCCGAGG3′; SEQ ID NO: 28) andHu3PCR-EcoRI (5′GAATTCCTATGTTCGGTAATTAATGGAAATTG3′; SEQ ID NO: 29).Three different libraries were constructed from the wild-type segmentsobtained by the PCR of the ¹⁰Fn3 clone and from randomized segmentsobtained by oligonucleotide synthesis. The BC_(r)-DE_(r)-FG_(r) librarywas obtained by randomizing the selected residues in BC, DE, and FGloops; the BC_(r)-DE_(wt)-FG_(r) library was obtained by randomizing theselected residues in BC and FG loops, leaving the DE loop sequencewild-type; and the BC_(wt)-DE_(wt)-FG_(r) library was obtained byrandomizing the selected residues in the FG loop only.

The BC_(r), DE_(r), and FG_(r) fragments were made synthetically. Eachfragment was assembled from two overlapping oligonucleotides, which werefirst annealed, then extended to form the double-stranded DNA form ofthe fragment. The oligonucleotides that were used to construct andprocess the three fragments are listed below; the “Top” and “Bottom”species for each fragment are the oligonucleotides that contained theentire ¹⁰Fn3 encoding sequence. In these oligonucleotides designations,“N” indicates A, T, C, or G; and “S” indicates C or G.

HfnLbcTop (His): (SEQ ID NO: 1)5′-GG AAT TCC TAA TAC GAC TCA CTA TAG GGA CAA TTACTA TTT ACA ATT ACA ATG CAT CAC CAT CAC CAT CACGTT TCT GAT GTT CCG AGG GAC CTG GAA GTT GTT GCT GCG ACC CCC ACC AGC-3′HfnLbcTop (an alternative N-terminus): (SEQ ID NO: 2)5′-GG AAT TCC TAA TAC GAC TCA CTA TAG GGA CAA TTACTA TTT ACA ATT ACA ATG GTT TCT GAT GTT CCG AGGGAC CTG GAA GTT GTT GCT GCG ACC CCC ACC AGC-3′ HFnLBCBot-flag8:(SEQ ID NO: 3) 5′-AGC GGA TGC CTT GTC GTC GTC GTC CTT GTA GTC GCTCTT CCC TGT TTC TCC GTA AGT GAT CCT GTA ATA TCT(SNN)₇ CCA GCT GAT CAG TAG GCT GGT GGG GGT CGC AGC-3′ HFnBC3′-flag8:(SEQ ID NO: 4) 5′-AGC GGA TGC CTT GTC GTC GTC GTC CTT GTA GTC GCTCTT CCC TGT TTC TCC GTA AGT GAT CC-3′ HFnLDETop: (SEQ ID NO: 5)5′- GG AAT TCC TAA TAC GAC TCA CTA TAG GGA CAA TTACTA TTT ACA ATT ACA ATG CAT CAC CAT CAC CAT CACCTC TTC ACA GGA GGA AAT AGC CCT GTC C-3′ HFnLDEBot-flag8: (SEQ ID NO: 6)5′-AGC GGA TGC CTT GTC GTC GTC GTC CTT GTA GTC GCT CTT CGT ATA ATC AAC TCC AGG TTT AAG GCC GCT GAT GGT AGC TGT (SNN)₄ AGG CAC AGT GAA CTC CTG GAC AGGGCT ATT TCC TCC TGT-3′ HFnDE3′-flag8: (SEQ ID NO: 7)5′-AGC GGA TGC CTT GTC GTC GTC GTC CTT GTA GTC GCTCTT CGT ATA ATC AAC TCC AGG TTT AAG G-3′ HFnLFGTop: (SEQ ID NO: 8)5′-GG AAT TCC TAA TAC GAC TCA CTA TAG GGA CAA TTA CTA TTT ACA ATT ACA ATG CAT CAC CAT CAC CAT CAC CTC TTC TAT ACC ATC ACT GTG TAT GCT GTC-3′ HFnLFGBot-flag8:(SEQ ID NO: 9) 5′-AGC GGA TGC CTT GTC GTC GTC GTC CTT GTA GTC TGTTCG GTA ATT AAT GGA AAT TGG (SNN)₁₀ AGT GAC AGC ATACAC AGT GAT GGT ATA-3′ HFnFG3′-flag8: (SEQ ID NO: 10)5′-AGC GGA TGC CTT GTC GTC GTC GTC CTT GTA GTC TGT TCG GTA ATT AAT GGA AAT TGG-3′T7Tmv (introduces T7 promoter and TMV untranslatedregion needed for in vitro translation): (SEQ ID NO: 11)5′- GCG TAA TAC GAC TCA CTA TAG GGA CAA TTA CTA TTT ACA ATT ACA-3′ASAflag8: (SEQ ID NO: 12)5′-AGC GGA TGC CTT GTC GTC GTC GTC CTT GTA GTC-3′Unispl-s (spint oligonucleotide used to ligate mRNA to the puromycin-containing linker, describedby Roberts et al, 1997, supra): (SEQ ID NO: 13)5′-TTTTTTTTTNAGCGGATGC-3′ A18---2PEG (DNA-puromycin linker):(SEQ ID NO: 14) 5′-(A)₁₈(PEG)₂CCPur

The oligonucleotide pair BC_(Top) and BC_(Bot-flag8) was used toconstruct the fragment which contains the randomized BC loop; the pairDE_(Top) and DE_(Bot-flag8) was used to construct the fragment whichcontains the randomized DE loop; the pair BC_(Top) and DE_(3-Flag8) wasused to PCR-amplify the BC_(wt)-DE_(wt) fragments; and the pair FG_(Top)and FG_(Bot-Flag8) was used to construct the fragment which contains therandomized FG loop. The pairs of oligonucleotides (500 pmol of each)were annealed in 100 μL of 10 mM Tris 7.5, 50 mM NaCl for 10 minutes at85° C., followed by a slow (0.5-1 hour) cooling to room temperature. Theannealed fragments with single-stranded overhangs were then extendedusing 100 U Klenow (New England Biolabs, Beverly, Mass.) for each 100 μLaliquot of annealed oligos, and the buffer made of 838.5 μl H₂O, 9 μl 1M Tris 7.5, 5 μl 1M MgCl₂, 20 μl 10 mM dNTPs, and 7.5 μl 1M DTT. Theextension reactions proceeded for 1 hour at 25° C.

In order to reduce the frequency of stop codons introduced by the randomsequences, the randomized residues were encoded by (NNS)_(n), where Nstands for any nucleotide and S for an equimolar mixture of C and G;only one of the three stop codons (TAG) conforms to the NNS restriction.In addition to the sequence encoding ¹⁰Fn3, the gene fragments containedthe 5′ Tobacco Mosaic Virus (TMV) untranslated region and the T7promoter, as well as the sequences encoding a 5′ hexahistidine proteinpurification tag and a 3′ FLAG epitope purification tag. In addition, asnoted above, Ear I restriction endonuclease recognition sites wereengineered into the overlaps between adjacent fragments in order tofacilitate the assembly of the three fragments.

Next, each of the double-stranded fragments was transformed into anRNA-protein fusion (PROfusion™) using the technique developed by Szostaket al., U.S. Ser. No. 09/007,005 and U.S. Ser. No. 09/247,190; Szostaket al., WO98/31700; and Roberts & Szostak, Proc. Natl. Acad. Sci. USA(1997) vol. 94, p. 12297-12302. Briefly, the fragments were transcribedusing an Ambion in vitro transcription kit, T7-MEGAshortscript™ (Ambion,Austin, Tex.), and the resulting mRNA was gel-purified and ligated to a5′-phosphorylated DNA-puromycin linker, preferably, 5′ dA₁₈PEG₂dCdCPur)using DNA ligase (Promega, Madison, Wis.); the mRNA was aligned with theDNA linker using a DNA splint oligonucleotide (5′ TTTTTTTTTNAGCGGATGC3′; SEQ ID NO: 30) as described in Szostak (supra). ThemRNA-DNA-puromycin molecule was then translated using the Ambion rabbitreticulocyte lysate-based translation kit in the presence of³⁵S-methionine. The resulting mRNA-DNA-puromycin-protein fusion waspurified using Oligo(dT) cellulose, (Type 7, Amersham Pharmacia,Piscataway, N.J.) and a complementary DNA strand was synthesized usingreverse transcriptase (Superscript™II, Gibco, Life Technologies,Rockville, Md.) and the RT primers described above (Unisplint-S orflagASA), following the manufacturer's instructions (preferably, atwo-minute annealing at 70° C. and a 40 minute reaction at 42° C.).

The RNA-protein fusion with annealing cDNA obtained for each fragmentwas next purified on the resin appropriate to its peptide purificationtag, i.e., on Ni-NTA agarose (Qiagen, Valencia, Calif.) for the His₆-tagand M2 Anti-Flag Agarose (Sigma, St. Louis, Mo.) for the FLAG-tag,following the procedures recommended by the manufacturers. Thefragment-encoding genetic information recovered by KOH elution wasamplified by PCR using Pharmacia Ready-to-Go PCR Beads, 10 pmol of 5′and 3′ PCR primers, and the following PCR program (Pharmacia,Piscataway, N.J.): Step 1: 95° C. for 3 minutes; Step 2: 95° C. for 30seconds, 58/62° C. for 30 seconds, 72° C. for 1 minute, 20/25/30 cycles,as required; Step 3: 72° C. for 5 minutes; Step 4: 4° C. until end(typically, 25 cycles).

The resulting DNA was cleaved by 5-6 U Earl (New England Biolabs) permDNA; the reaction took place in T4 DNA Ligase Buffer (New EnglandBiolabs) at 37° C., for 1 hour, and was followed by an optionalincubation at 70° C. for 15 minutes to inactivate Ear I. Equal amountsof the BC, DE, and FG fragments were combined and ligated to form afull-length ¹⁰Fn3 gene with randomized loops. The ligation required 10 Uof fresh Earl (New England Biolabs) and 20 U of T4 DNA Ligase (Promega,Madison, Wis.), and took 1 hour at 37° C. Earl and ligase were theninactivated by a 15 minute incubation at 65° C.

Three different libraries, BCwt-DEwt-FGr, BCr-DEwt-FGr, and BCr-DEr-FGr,were made in the manner described above. Each contained the form of theFG loop with 10 randomized residues. The BC and the DE loops of thefirst library bore the wild type ¹⁰Fn3 sequence; a BC loop with 7randomized residues and a wild type DE loop made up the second library;and a BC loop with 7 randomized residues and a DE loop with 4 randomizedresidues made up the third library. The complexity of the FG loop ineach of these three libraries was 10¹³; the further two randomized loopsprovided the potential for a complexity too large to be sampled in alaboratory. The combination of these libraries provided a master libraryhaving 10¹² unique clones.

The sequences of 76 randomly picked clones from the original,randomized, BC_(r)-DE_(r)-FG_(r) library showed no pattern in therandomized loops (data not shown); the amino acid frequency in thelibrary varied in proportion to the number of codons available thatencoded each residue, between 1% per position (glutamic acid,methionine, tryptophan) and 14% per position (proline). In contrast, theaverage probability for a residue in the preserved, beta-sheet frameworkto have remained as wild type was found to be 99%.

Equimolar amounts of the three libraries (2 pmoles of DNA each) werecombined into one master library in order to simplify the selectionprocess; target binding itself was expected to select the most suitablelibrary for a particular challenge. RNA-protein fusions were obtainedfrom the master library following the general procedure described inSzostak et al., U.S. Ser. Nos. 09/007,005 and 09/247,190; Szostak etal., WO98/31700; and Roberts & Szostak, Proc. Natl. Acad. Sci. USA(1997) vol. 94, p. 12297-12302 (FIG. 8), except that affinitypurification performed in rounds three to ten used only M2-Sepharose(see below).

Fusion Selections

The master library in the RNA-protein fusion form was subjected toselection for binding to TNF-α (Pepro Tech, Rocky Hill, N.J.). Twoinitial protocols were employed: one in which the target was immobilizedon an agarose column and one in which the target was immobilized on aBIACORE chip. First, an extensive optimization of conditions to minimizebackground binders to the agarose column yielded the favorable bufferconditions of 50 mM HEPES pH 7.4, 0.02% Triton, 100 μg/ml sheared salmonsperm DNA. In this buffer, the non-specific binding of the ¹⁰Fn3-RNAfusion to TNF-α Sepharose was 0.3%. The non-specific binding backgroundof the ¹⁰Fn3-RNA/cDNA library to TNF-α Sepharose was found to be 0.1%.

During each round of selection on TNF-α Sepharose, the library was firstpreincubated for an hour with underivatized Sepharose to remove anyremaining non-specific binders; the flow-through from this pre-clearingwas incubated for another hour with TNF-α Sepharose. The TNF-α Sepharosewas washed for 3-30 minutes.

After each selection, the cDNA component of the complex that had beeneluted from the solid support with 0.3 M NaOH or 0.1M KOH was amplifiedby PCR; a DNA band of the expected size persisted through multiplerounds of selection (FIG. 9); similar results were observed in the twoalternative selection protocols, and only the data from the agarosecolumn selection is shown in FIG. 9.

In this selection, in the first seven rounds, the binding ofFn3-RNA/cDNA molecules to the target remained low; in contrast, whenfree protein was translated from DNA pools at different stages of theselection, the proportion of the column binding species increasedsignificantly between rounds (FIG. 10).

In later selections, the fusion pools selected in the first eight roundsof selection (R1-8) bound to TNF-α-Sepharose at levels close to thebackground (<0.25%) (FIG. 13). After nine rounds of selection (R9), thebinding of fusion to TNF-α-Sepharose increased sharply to 0.7%, and,after ten rounds of selection (R10), the binding increased further to 7%(FIG. 13). These selections were carried out using TNF-α immobilized onEpoxy-Activated Sepharose™ 6B (Amersham Pharmacia) at 10 mg TNF/gSepharose in 10 mL. Before use, the TNF-α-derivatized Sepharose wasblocked in Binding Buffer (50 mM HEPES, pH 7.4, 0.02% Triton, 0.1 mg/mLsheared salmon sperm DNA (Ambion)), overnight, at 4° C.

The ¹⁰Fn3-based master library was transcribed, ligated to thepuromycin-bearing linker, translated into an mRNA-protein library in thepresence of 5-10 μL/300 μL ³⁵S-methionine, affinity purified onOligo(dT) Cellulose, reverse-transcribed into a DNA/mRNA-proteinlibrary, and affinity-purified on M2-Sepharose (for rounds 3-10), asdescribed above. Forty pmol of DNA/mRNA-protein fusion librarymolecules, the equivalent of 20 copies of 4×10¹² different sequences,were recovered, then subjected to the first round (R1) of the selection.

In the first step of the selection, 40 pmoles of the DNA/mRNA-proteinlibrary was incubated for 1 hour at 4° C., with tumbling, in 300 μL ofBinding Buffer with 30 μL of Epoxy-Sepharose that had been subjected tothe derivatization procedure in the absence of TNF-α. In the secondround, 24 pmol of the library was added, and in the remaining eightrounds, 0.1-2 pmol of the library was added. The supernatant wasrecovered by microcentrifugation through a Micro Bio-Spin®chromatography column (BIO-RAD, Hercules, Calif.), then incubated with30 μL of TNF-α-Sepharose (6 μM) in 300 μL of the Binding Buffer for 1hour at 4° C. (during Rounds 7-10, the Binding Buffer contained anadditional 1 mg/mL of BSA). The TNF-α-Sepharose was recovered on a spincolumn, then washed with 3×300 μL of Binding Buffer, eluted with 100 μLof 0.1 M KOH, and finally neutralized with 1 μL of 1 M Tris 8.0, 8 μL of1 M HCl. Samples of the library, of the TNF-α-Sepharose before and afterthe elution, of the washes, and of the elutions were quantified bycounting ³⁵S-methionine in the sample in a scintillation counter. Thenext round of selection began with the formation of a newDNA/mRNA-protein pool by PCR amplification, which was transcribed,translated, and reverse-transcribed from the PCR product.

The DNA pools obtained from the elution after nine and after ten roundswere cloned into the TOPO™ TA®, pCR2.1 cloning vector (Invitrogen,Carlsbad, Calif.) and transformed into E. coli. Between 30 and 100clones were picked and grown into plasmid minipreps (Qiagen).Thirty-eight clones from R9 and 29 clones from R10 were picked at randomand sequenced (DNA Sequencing Core Facility, Massachusetts GeneralHospital, Dept. of Molecular Biology, Boston, Mass.). The programClustalW⁶⁰ was used to align the resulting protein sequences.

Amino Acid Residue Sequences of the TNF-α Binding Clones

Thirty-eight of the 61 clones derived from R9 and from R10 had uniqueamino acid sequences, a surprising diversity. The ten clones that wereisolated more than once, presumably because of their superior binding toTNF-α, are listed in Table 1 (full sequences in FIG. 25).

Of the 61 clones picked randomly from the winning pool, only one (cloneT09.08, sequence not shown) had its origin in the BC_(wt)-DE_(wt)-FG_(r)library, with another six from the BC_(r)-DE_(wt)-FG_(r) library. Theobservation that the remaining 54 (88% of the winners) were selectedfrom the BC_(r)-DE_(r)-FG_(r) library points out the importance forTNF-α cooperative binding of the target by several loops.

The most common motif found in the selected loop sequences is PWA(S/T),which is found in the DE loop of 33 of the 61 clones; the more looselydefined sequence of PW(A/G) is seen in 41/61 clones. Such a strongselection for a specific DE sequence is surprising since the analogousCDR-H2 loops of antibody V_(H) domains generally make only a smallcontribution to antigen binding. On the other hand, the short length ofthe DE loop, which means that 10⁷ copies of each possible tetrapeptidesequence would be expected to be present in the library, wouldfacilitate the optimization of any contribution of the DE loop to theselected properties. A survey of other Fn3 domains (Dickenson et al., J.Mol. Biol. 236:1079-1092 (1994)) shows that proline is found atpositions equivalent to the ¹⁰Fn3 residue 52 as frequently as is thewild-type glycine; similarly, alanine, glycine, and the wild-type lysineare all common at positions equivalent to the ¹⁰Fn3 position 54. Inconsequence, it appears likely that the selected residues at positions52 and 54 are at least consistent with favorable biophysical properties.In contrast, no tryptophan is found at the position equivalent to the¹⁰Fn3 residue 53, which suggests that Tryptophan 53 may have beenselected for a reason specific to the present selection, such as due toa contribution to TNF-α binding. This is consistent with the absence ofthis motif in later selections against other antigens, again suggestingthat the PWA/G motif is more likely to contribute to TNF-α bindingdirectly than through stability or solubility of the ¹⁰Fn3 domain. Thepreference for the PWA/G motif on loop DE suggests another possiblereason for the preference for the BC_(r)-DE_(r)-FG_(r) library duringthe selection: the BC_(r)-DE_(r)-FG_(r) library alone contained therandomized DE loop, and would be expected to outcompete the other twolibraries if the PWA/G sequence were important to target binding.

The sequences selected most frequently in the BC loop is NRSGLQS (12/61)(SEQ ID NO: 31), whereas the sequence selected most commonly in the FGloop is AQTGHHLHDK (6/61) (SEQ ID NO: 32). An NRSGLQS BC loop and anAQTGHHLHDK FG loop have not been found in the same molecule, but twoclones were found which contain the most frequently isolated sequenceson two of the three randomized loops. These clones, T10.06 (BC: NRSGLQS,DE: PWA) and T09.12 (DE: PWA, FG: AQTGHHLHDK), have two of the lowestfour dissociation constants from TNF-α of the clones examined (Table 1).

Due to the use of a Taq polymerase that contains no proofreadingactivity, every round of PCR introduced additional random mutations intoboth the CDR-like loops and the beta-sheet scaffold of the ¹⁰Fn3sequence, at the estimated rate of 0.01% per base pair, i.e., 3% per¹⁰Fn3 gene per round of PCR and approximately 75% per round ofselection. Consequently, it is likely that the residues preserved aswild-type and those preserved in a non-wild-type stable sequenceindicate that such sequences were selected due to their superiorproperties. In the mutated loops, it is impossible to distinguishbetween the mutations introduced by oligonucleotide synthesis or by PCRmutagenesis, but in the beta-strand scaffold, most of the mutationsselected originate from Taq errors. The selected clones showed severalconserved changes in the scaffold of the protein, which had not beenrandomized intentionally. FIG. 18 indicates the residues in the ¹⁰Fn3beta sheet that had not been randomized, but nevertheless mutated duringselection. This mutagenesis occurred at the frequency of 26-28 of the 61clones; these mutations are marked with arrows under the wild-type ¹⁰Fn3sequence and with the letter that identifies the selected residue. Inparticular, 28 of the 61 clones mutated from Leucine 18 to Arginine orto Glutamine, and 26 clones mutated from Threonine 56 to Isoleucine.FIG. 19 shows the location of these scaffold mutations. Whereas position56 is at the stem loop DE and thus would be expected to affect theconformation and the target-binding properties of this loop, thedistance of position 18 from the presumed TNF-α-binding loops suggeststhat the selective advantage of this mutation may arise from an indirecteffect on the conformation of loop BC or from an effect on the stabilityof the protein (FIG. 19). This is supported by an experiment in whichclone T 10.06, which contains the frequently seen L18R and T56I changesfrom the wild-type, was mutagenized to reverse position 18 back to thewild-type leucine. This change caused an increase of the K_(d) of thevariant by approximately 10-fold. The weaker binding of the T10.06(L18)protein to TNF-α suggests that the residue at position 18 has an effecton the binding of the target by the CDR-like loops, possibly by a minorstructural change that is transmitted through the beta-strand to loopBC.

Affinity and Specificity of the Selected TNF-α Binding Pools

The apparent average K_(d) values of free protein pools for TNF-α afternine and after ten rounds of selection were found to beindistinguishable (4 and 6 nM, respectively; Table 1); this similarityin affinity is consistent with the relatively low (10 fold) level ofenrichment observed in the last round of selection and with thesimilarity in the sequence composition of the two pools. The apparentaverage K_(d) values of free protein pool after four further rounds ofselection was 3 nM, also indistinguishable from those of R9 and R10pools

In order to assess the specificity of the binding of the pool selectedafter ten rounds of selection, we compared the binding of two differentfree protein pools to three cytokines immobilized on Sepharose to TNF-α,the target of the selection, and to IL-la and IL-13, which wereirrelevant to the selection. The first pool had been transcribed andtranslated from the initial, randomized DNA library before the selection(R0), and the second pool, from the library after ten rounds ofselection (R10).

To carry out these experiments, the PCR product of the elution after thetenth round of selection was transcribed and translated in vitro, in thepresence of ³⁵S-methionine but without forming the mRNA-protein fusion.The resulting fraction of the free protein bound to TNF-α-Sepharose, toIL-1α-Sepharose, to IL-13-Sepharose at approximately 10 μM, 30 μM, and50 μM, respectively, and to underivatized Sepharose was compared (FIG.20), using the procedure described above for DNA/mRNA-protein fusionbinding to TNF-α-Sepharose. The amount of the selected pool bound toeach of the targets was measured by scintillation counting of the washedbeads.

FIG. 20 shows that, whereas the binding of R0 to TNF-α, IL-1α, and IL-13was similar (2%, 4%, and 3%, respectively), the ten rounds of selectionresulted in 32% binding to the targeted TNF-α, in 3% binding to IL-1α,and in 1% binding to IL-13. The absolute and the relative increase ofprotein binding to TNF-α demonstrates the ability of the ¹⁰Fn3 scaffoldand of the DNA/mRNA-protein fusion-based selection system to selecttarget-specific binders.

To examine the specificity of binding further, clone T09.12 wasimmobilized in a microarray format (as generally described below) andwas tested for binding to soluble TNF-α. Specific binding of TNF-α tothis clone was detected using fluorescence detection (FIG. 24A) and massspectroscopy (FIG. 24B). For the mass spectroscopy results, bindingassays were carried out in the presence of fetal bovine serum, anexemplary complex biological fluid containing a variety of potentialinterfering proteins. For fluorescence detection (FIG. 24A), a mixtureof RNA-¹⁰Fn3 fusion of wild-type ¹⁰Fn3 and of the T09.12 variant(Table 1) was hybridized onto a DNA microarray on which oligonucleotidescomplementary to the RNA portion of the fusion molecules had beenimmobilized at 600 micron pitch, with 24 replicate features. Afterremoval of unhybridized fusion by washing, the surface was exposed tobiotin-TNF-α (2.6 μg/mL in TBS, 0.02% Tween-20, 0.2% BSA), washed, andair-dried. The captured biotin-TNF-α was detected by Cy3-labeledanti-biotin monoclonal antibody (Sigma) using a ScanArray 5000 system(GSI Lumonics). For mass spectroscopy detection, RNA-¹⁰Fn3 fusion of theT09.12 variant (FIG. 24B) and wild-type ¹⁰Fn3 (FIG. 24C) was treatedwith RNase A to generate a fusion between the protein and the DNAlinker. The resulting DNA-linked protein was hybridized to a glasscoverslip arrayed with an immobilized oligonucleotide complementary tothe DNA linker (FIGS. 24B and 24C; no fusion was applied in FIG. 24D).After washing, the above surfaces were exposed to TNF-α (1.5 mg/mL in90% v/v PBS/10% fetal bovine serum). The dried chip was spotted withMALDI matrix and analyzed with a Voyager DE MALDI-TOF mass spectrometer(PerSeptive Biosystems). A signal at 17.4 kD, which corresponded to theexpected molecular mass of monomeric TNF-α, was detected on the 200 μmfeatures that contained T09.12 protein (FIG. 24A), but not on thefeatures that contained wild-type ¹⁰Fn3 (FIG. 24B) nor on the featuresthat did not contain DNA-protein fusion (FIG. 24C).

K_(d) of the Selected TNF-α Binding Clones

Dissociation constants were determined for all the clones that wererepresented more than once in the two pools generated after nine andafter ten rounds of selection, as well as for the only clone thatoriginated from the BC_(wt)-DE_(wt)-FG_(r) library (clone T09.08).

To determine these binding constants, biotinylated TNF-α was preparedusing the NHS-LC-LC-Biotin reagent supplied by Pierce (Rockford, Ill.).MALDI-TOF mass spectrometry was used to estimate that more than 80% ofthe monomeric TNF-α, and hence more than 99% of the trimer, wasbiotinylated.

For the R9 and R10 pools (and the R14 and M12 pools discussed below), aswell as for the characterized clones derived from these two pools,eleven samples of 0.25 nM, in vitro-translated, ³⁵S-methionine-labeledfree protein were incubated with the biotinylated TNF-α at aconcentration between 17 pM and 23 nM, in 200 μL 10 mM HEPES, pH 7.4,150 mM NaCl, 1% BSA, 0.02% Triton, for one hour at room temperature.Subsequently, each sample was loaded on a pre-soaked, SAM^(2R) BiotinCapture Membrane (Promega, Madison, Wis.) using a 96 well, Easy-Titer™ELIFA system (Pierce). Under vacuum, each spot was washed with 200 μL ofHBS pH 7.4, 1% BSA, 0.05% Triton; next the entire membrane was rinsed inthe buffer and air-dried. The membrane was exposed with a StoragePhosphor Screen (Molecular Dynamics, Sunnyvale, Calif.) overnight, andthe intensities of the resulting individual spots were quantified usinga STORM 860 phosphoimager with the ImageQuaNT densitometry program(Molecular Dynamics). The K_(d) of the binding was determined by fittingthe equilibrium equation to the resulting binding curve (KaleidaGraph,Synergy Software); the error of the experiment was estimated from 2-4independent experiments.

In these studies, the K_(d) values were found to be in the narrow rangeof 1-24 nM (Table 1). The T09.12 and T10.06 clones, which contained themost commonly isolated sequences in two loops each, have the low K_(d)of 4 and 2 nM, respectively; on the other hand, a number of clones withless frequently seen loops, such as clones T09.07 and T10.15, showedsimilarly tight binding.

A sample comparison of TNF-α binding between free protein and thecDNA/mRNA-protein complex derived from the same sequence showed that thetwo dissociation constants were within experimental error of each other,a property of the system that makes it possible to use thecDNA/mRNA-protein complex to select for target-binding properties of theprotein itself.

High-Stringency Selection of TNF-α Binding Clones

Despite the duplicate clones isolated, the TNF-α-binding pools afternine and after ten rounds of selection contained numerous differentclones, i.e., 38 different sequences in 61 clones sampled. Therefore,further selection, with more stringent binding requirements, wasundertaken to recover a subset of these clones with superior TNF-αbinding properties. Consequently, four further rounds of selections(R11-R14) were conducted in solution, where the concentration of thetarget was controlled more easily. The concentration of TNF-α waslimited to 0.5 nM and the concentration of DNA/mRNA-¹⁰Fn3 pool to 0.1nM; in addition, the length and the temperature of the washes of the¹⁰Fn3/TNF-α complex bound to streptavidin-coated paramagnetic beads wereincreased.

Specifically, these selections were carried out as follows. For rounds11-13, 0.1 nM DNA/mRNA-¹⁰Fn3 fusion library, which had been made asdescribed above, was pre-cleared by tumbling for 1 hour at 4° C. with100 μL of Dynabeads® M-280 (streptavidin-coated paramagnetic beads;Dynal, Lake Success, N.Y.) that had been pre-blocked in Binding Buffer.The resulting pre-cleared fusion mixture was combined with 0.5 nMbiotinylated TNF-α in 300 μL of the above Binding Buffer, and thecomplex incubated at 4° C. for 1 hour. Next, 100 μl of resuspendedDynabeads® M-280 Streptavidin at 1.3 g/cm³, which had been blocked byovernight incubation in Binding Buffer, were added to the mixture andincubated at 4° C., with tumbling, for 45 additional minutes. Theparamagnetic beads were separated from the supernatant on a Dynal MPC-Srack, the supernatant was removed, and the beads were washed with theBinding Buffer for 1, 15, and 30 minutes in the case of R11 and R12, orfor 1 minute, followed by nine ten-minute washes in the case of R13-R14.DNA was eluted from the washedDNA/mRNA-¹⁰Fn3:TNF-α-biotin:streptavidin-bead complexes with two washesof 100 μL 0.1 M KOH, and treated as described above for the column-basedselection to produce the next generation DNA/mRNA-¹⁰Fn3 fusion library.Round 14 differed from R11-R13 in that the selection was performed at30° C. and in the presence of an additional 150 mM NaCl. Except for theelevated temperature, the sequence of washes was the same for R14 as forR13.

Twenty-two clones derived from the DNA eluted after four further roundsof selection (R14) were picked at random and found to represent 15different loop sequences (Table 2; full sequences in FIG. 25). The cloneT10.06, isolated previously from R10 as described above, was pickedeight separate times, whereas the remaining sequences, including T09.31,which had been isolated from the R9 pool, were found in one isolateeach. Similar to the isolates from rounds nine and ten, the R14 clonesexamined showed a preference (18 of 22 clones) for the PWA/G sequence inthe DE loop, and four new, non-wild-type DE sequences were revealed.

Whereas the apparent average K_(d) values of the R14 free protein pool,3 nM, is similar to those measured for the pools after nine and tenrounds (4 and 6 nM, respectively), several K_(d) values of the clonesisolated from the R14 pool were an order of magnitude lower than thelowest values observed in the R9 and R10 pools (Table 2). The clonesthat bound TNF-α most tightly, T14.07 and T 14.25, had a K_(d) of 90pmol. Thus, the conditions used in the last four rounds of selectionswere stringent enough to favor ¹⁰Fn3 molecules with subnanomolar K_(d),but not so stringent as to eliminate such molecules.

5 Mutagenic Affinity Maturation

As discussed above, the selections described herein may also be combinedwith mutagenesis after all or a subset of the selection steps to furtherincrease library diversity. In one parallel selection strategy,error-prone PCR was incorporated into the amplification of DNA betweenrounds (Cadwell and Joyce, PCR Methods Appl 2:28 (1992)). This techniquewas carried out beginning with the diverse DNA pool eluted after R8above. This pool was amplified using error-prone PCR, with the pooldivided into seven equal parts and mutagenized at the target frequencyof 0.8%, 1.6%, 2.4%, 3.2%, 4.0%, 4.8%, and 5.6%. The seven PCR reactionswere combined, and cDNA/RNA-protein fusion was made from the mixture andsubjected to a round of selection in solution. Before the secondmutagenic round, M10, error-prone PCR was performed in three separatereactions, at 0.8%, 1.6%, and 2.4%. The two remaining rounds, M11 andM12, were performed using standard Taq PCR. Except for mutagenesis, theselection conditions for M9-M12 were the same as for R11-R14. The twentyM12 clones tested showed tighter binding to TNF-α than the clonesselected using the two earlier selection protocols (Table 3; fullsequences in FIG. 25); the tightest binding of TNF-α was seen in M12.04,and had the observed K_(d) of 20 pM. These results demonstrated thatlow-level, random mutagenesis late in a selection can improve both thebinding affinity of selected antibody mimics (20 pM vs. 90 pM) and thespeed with which they can be selected (12 rounds vs. 14 rounds). Inaddition, the frequency of tight binders in this mutagenesis approachwas observed to be about 5%, whereas the frequency is approximately 3%in other selections.

Superiority of Fn Binders

The selection of ¹⁰Fn3 variants capable of binding to TNF-α, performedusing covalent mRNA-protein fusion as the unit of selection, was won bymolecules with dissociation constants as low as 20 pM. These K_(d)values compared favorably against the standards of selection of othersthat used other antibody mimic scaffolds and selection methods.Consequently, the ¹⁰Fn3-based scaffold and covalent mRNA-proteinfusion-based in vitro selection method may be utilized for thedevelopment of antibody mimics against a broad range of antigens. Inaddition, the subnanomolar, TNF-α-binding ¹⁰Fn3 variants describedherein represent potential therapeutic, research, and diagnostic agents.Moreover, since this in vitro selection method can be automated, such acombination of scaffold and selection methods have applications on thegenomic scale.

One of the factors that contributed to the success of the presentselection was the randomization of all three CDR-like loops of ¹⁰Fn3;similar libraries which contained only one or two randomized loops wereless likely to include tight binders than the library with threerandomized, CDR-like loops.

In the selection reported above, the randomized loops remained thelength of the corresponding, wild-type ¹⁰Fn3 loops. To generate furtherlibrary diversity, the length of the loops as well as their sequencesmay be varied, to incorporate favorable mutations in the ¹⁰Fn3beta-sheet into the wild-type scaffold used for library construction,and to create libraries with randomized beta-sheet scaffolds which willallow selection of structures even more successful at mimickingantibodies.

Selections similar to those described herein may be carried out with anyother binding species target (for example, IL-1 or IL-13).

Animal Studies

Wild-type ¹⁰Fn3 contains an integrin-binding tripepetide motif, Arginine78-Glycine 79-Aspartate 80 (the “RGD motif”) at the tip of the FG loop.In order to avoid integrin binding and a potential inflammatory responsebased on this tripeptide in vivo, a mutant form of ¹⁰Fn3 was generatedthat contained an inert sequence, Serine 78-Glycine 79-Glutamate 80 (the“SGE mutant”), a sequence which is found in the closely related,wild-type ¹¹Fn3 domain. This SGE mutant was expressed as an N-terminallyHis₆-tagged, free protein in E. coli, and purified to homogeneity on ametal chelate column followed by a size exclusion column.

In particular, the DNA sequence encoding His₆-¹⁰Fn3(SGE) was cloned intothe pET9a expression vector and transformed into BL21 DE3 pLysS cells.The culture was then grown in LB broth containing 50 μg/mL kanamycin at37° C., with shaking, to A₅₆₀=1.0, and was then induced with 0.4 mMIPTG. The induced culture was further incubated, under the sameconditions, overnight (14-18 hours); the bacteria were recovered bystandard, low speed centrifugation. The cell pellet was resuspended in1/50 of the original culture volume of lysis buffer (50 mM Tris 8.0, 0.5M NaCl, 5% glycerol, 0.05% Triton X-100, and 1 mM PMSF), and the cellswere lysed by passing the resulting paste through a MicrofluidicsCorporation Microfluidizer M110-EH, three times. The lysate wasclarified by centrifugation, and the supernatant was filtered through a0.45 μm filter followed by filtration through a 0.2 μm filter. 100 mL ofthe clarified lysate was loaded onto a 5 mL Talon cobalt column(Clontech, Palo Alto, C A), washed by 70 mL of lysis buffer, and elutedwith a linear gradient of 0-30 mM imidazole in lysis buffer. The flowrate through the column through all the steps was 1 mL/min. The elutedprotein was concentrated 10-fold by dialysis (MW cutoff=3,500) against15,000-20,000 PEG. The resulting sample was dialysed into buffer 1(lysis buffer without the glycerol), then loaded, 5 mL at a time, onto a16×60 mm Sephacryl 100 size exclusion column equilibrated in buffer 1.The column was run at 0.8 mL/min, in buffer 1; all fractions thatcontained a protein of the expected MW were pooled, concentrated 10× asdescribed above, then dialyzed into PBS. Endotoxin screens and animalstudies were performed on the resulting sample (Toxikon; MA).

The endotoxin levels in the samples examined to date have been below thedetection level of the assay. In a preliminary animal toxicology study,this protein was injected into two mice at the estimated 100×therapeutic dose of 2.6 mg/mouse. The animals survived the two weeks ofthe study with no apparent ill effects. These safety results support theuse of ¹⁰Fn3 incorporated into an IV drug.

Alternative Constructs for In Vivo Use

To extend the half life of the 8 kD ¹⁰Fn3 domain, a larger molecule hasalso been constructed that mimics natural antibodies. This ¹⁰Fn3-F_(c)molecule contains the —CH₁—CH₂—CH₃ (FIG. 11) or —CH₂—CH₃ domains of theIgG constant region of the host; in these constructs, the ¹⁰Fn3 domainis grafted onto the N-terminus in place of the IgG V_(H) domain (FIGS.11 and 12). Such antibody-like constructs are to improve thepharmacokinetics of the protein as well as its ability to harness thenatural immune response.

In order to construct the murine form of the ¹⁰Fn3-CH₁—CH₂—CH₃ clone,the —CH₁—CH₂—CH₃ region was first amplified from a mouse liver spleencDNA library (Clontech), then ligated into the pET25b vector. Theprimers used in the cloning were 5′ Fc Nest and 3′ 5 Fc Nest, and theprimers used to graft the appropriate restriction sites onto the ends ofthe recovered insert were 5′ Fc HIII and 3′ Fc Nhe:

5′ Fc Nest  (SEQ ID NO: 15)5′GCG GCA GGG TTT GCT TAC TGG GGC CAA GGG 3′; 3′ Fc Nest (SEQ ID NO: 16) 5′GGG AGG GGT GGA GGT AGG TCA CAG TCC 3′; 3′ Fc Nhe (SEQ ID NO: 17) 5′ TTT GCT AGC TTT ACC AGG AGA GTG GGA GGC 3′;  and 5′Fc HIII  (SEQ ID NO: 18) 5′AAA AAG CTT GCC AAA ACG ACA CCC CCA TCT GTC 3′.

Further PCR was used to remove the CH₁, region from this clone and tocreate the Fc part of the shorter, ¹⁰Fn3-CH₂—CH₃ clone. The sequenceencoding ¹⁰Fn3 was spliced onto the 5′ end of each clone; either thewild type ¹⁰Fn3 cloned from the same mouse spleen cDNA library or amodified ¹⁰Fn3 obtained by mutagenesis or randomization of the moleculescan be used. The oligonucleotides used in the cloning of murinewild-type ¹⁰Fn3 were:

Mo 5PCR-NdeI: (SEQ ID NO: 19) 5′ CATATGGTTTCTGATATTCCGAGAGATCTGGAG 3′;Mo5PCR-His-NdeI (for an alternative N-terminuswith the His6 purification tag): (SEQ ID NO: 20) 5′CAT ATG CAT CAC CAT CAC CAT CAC GTT TC GAT ATT CCG AGA G 3′;  andMo3PCR-EcoRI: (SEQ ID NO: 21)  5′ GAATTCCTATGTTTTATAATTGATGGAAAC3′.

The human equivalents of the clones are constructed using the samestrategy with human oligonucleotide sequences.

Antibody Mimics in Protein Chip Applications

Any of the antibody mimics described herein may be immobilized on asolid support, such as a microchip. The suitability of the presentscaffolds, for example, the ¹⁰Fn3 scaffold, for protein chipapplications is the consequence of (1) their ability to support manybinding functions which can be selected rapidly on the bench or in anautomated setup, and (2) their superior biophysical properties.

The versatile binding properties of ¹⁰Fn3 are a function of the loopsdisplayed by the Fn3 immunoglobulin-like, beta sandwich fold. Asdiscussed above, these loops are similar to the complementaritydetermining regions of antibody variable domains and can cooperate in away similar to those antibody loops in order to bind antigens. In oursystem, ¹⁰Fn3 loops BC (for example, residues 21-30), DE (for example,residues 51-56), and FG (for example, residues 76-87) are randomizedeither in sequence, in length, or in both sequence and length in orderto generate diverse libraries of mRNA-¹⁰Fn3 fusions. The binders in suchlibraries are then enriched based on their affinity for an immobilizedor tagged target, until a small population of high affinity binders aregenerated. Also, error-prone PCR and recombination can be employed tofacilitate affinity maturation of selected binders. Due to the rapid andefficient selection and affinity maturation protocols, binders to alarge number of targets can be-selected in a short time.

As a scaffold for binders to be immobilized on protein chips, the ¹⁰Fn3domain has the advantage over antibody fragments and single-chainantibodies of being smaller and easier to handle. For example, unlikesingle-chain scaffolds or isolated variable domains of antibodies, whichvary widely in their stability and solubility, and which require anoxidizing environment to preserve their structurally essential disulfidebonds, ¹⁰Fn3 is extremely stable, with a melting temperature of 110° C.,and solubility at a concentration>16 mg/mL. The ¹⁰Fn3 scaffold alsocontains no disulfides or free cysteines; consequently, it isinsensitive to the redox potential of its environment. A furtheradvantage of ¹⁰Fn3 is that its antigen-binding loops and N-terminus areon the edge of the beta-sandwich opposite to the C-terminus; thus theattachment of a ¹⁰Fn3 scaffold to a chip by its C-terminus aligns theantigen-binding loops, allowing for their greatest accessibility to thesolution being assayed. Since ¹⁰Fn3 is a single domain of only 94 aminoacid residues, it is also possible to immobilize it onto a chip surfaceat a higher density than is used for single-chain antibodies, with theirapproximately 250 residues. In addition, the hydrophilicity of the 10Fn3scaffold, which is reflected in the high solubility of this domain,minimizes unwanted binding of ¹⁰Fn3 to a chip surface.

The stability of the ¹⁰Fn3 scaffold as well as its suitability forlibrary formation and selection of binders are likely to be shared bythe large, Fn3-like class of protein domains with an immunoglobulin-likefold, such as the domains of tenascin, N-cadherin, E-cadherin, ICAM,titin, GCSF-R, cytokine receptor, glycosidase inhibitor, and antibioticchromoprotein. The key features shared by all such domains are a stableframework provided by two beta-sheets, which are packed against eachother and which are connected by at least three solvent-accessible loopsper edge of the sheet; such loops can be randomized to generate alibrary of potential binders without disrupting the structure of theframework (as described above). In addition, as with ¹⁰Fn3, any of theseloops (or similar loops from other proteins) may be immobilized alone orin combination with other loops onto a solid support surface.

Immobilization of Fn3-Based Antibody Mimics

To immobilize antibody mimics, such as Fn3-based antibody mimics, to achip surface, a number of exemplary techniques may be utilized. Forexample, such antibody mimics may be immobilized as RNA-protein fusionsby Watson-Crick hybridization of the RNA moiety of the fusion to a basecomplementary DNA immobilized on the chip surface (as described, forexample, in Addressable Protein Arrays, U.S. Ser. No. 60/080,686; U.S.Ser. No. 09/282,734; and WO 99/51773; and Methods for Encoding andSorting In Vitro Translated Proteins, U.S. Ser. No. 60/151,261 and U.S.Ser. No. 09/648,040). Alternatively, antibody mimics can be immobilizedas free proteins directly on a chip surface. Manual as well as roboticdevices may be used for deposition of the antibody mimics on the chipsurface. Spotting robots can be used for deposition of antibody mimicswith high density in an array format (for example, by the method ofLueking et al., Anal Biochem. 1999 May 15; 270(1):103-11). Differentmethods may also be utilized for anchoring the antibody mimic on thechip surface. A number of standard immobilization procedures may be usedincluding those described in Methods in Enzymology (K. Mosbach and B.Danielsson, eds.), vols. 135 and 136, Academic Press, Orlando, Fla.,1987; Nilsson et al., Protein Expr. Purif. 1997 October; 11(1):1-16; andreferences therein. Oriented immobilization of antibody mimics can helpto increase the binding capacity of chip-bound antibody mimics.Exemplary approaches for achieving oriented coupling are described in Luet al., The Analyst (1996), vol. 121, p. 29R-32R; and Turkova, JChromatogr B Biomed Sci App. 1999 Feb. 5; 722(1-2):11-31. In addition,any of the methods described herein for anchoring antibody mimics tochip surfaces can also be applied to the immobilization of antibodymimics on beads, or other supports.

Target Protein Capture and Detection

Selected populations of scaffold-binders may be used for detectionand/or quantitation of analyte targets, for example, in samples such asbiological samples. To carry out this type of diagnostic assay, selectedscaffold-binders to targets of interest are immobilized on anappropriate support to form multi-featured protein chips. Next, a sampleis applied to the chip, and the components of the sample that associatewith the binders are identified based on the target-specificity of theimmobilized binders. Using this technique, one or more components may besimultaneously identified or quantitated in a sample (for example, as ameans to carry out sample profiling).

Methods for target detection allow measuring the levels of bound proteintargets and include, without limitation, radiography, fluorescencescanning, mass spectroscopy (MS), and surface plasmon resonance (SPR).Autoradiography using a phosphorimager system (Molecular Dynamics,Sunnyvale, Calif.) can be used for detection and quantification oftarget protein which has been radioactively labeled, e.g., using ³⁵Smethionine. Fluorescence scanning using a laser scanner (see below) maybe used for detection and quantification of fluorescently labeledtargets. Alternatively, fluorescence scanning may be used for thedetection of fluorescently labeled ligands which themselves bind to thetarget protein (e.g., fluorescently labeled target-specific antibodiesor fluorescently labeled streptavidin binding to target-biotin, asdescribed below).

Mass spectroscopy can be used to detect and identify bound targets basedon their molecular mass. Desorption of bound target protein can beachieved with laser assistance directly from the chip surface asdescribed below. Mass detection also allows determinations, based onmolecular mass, of target modifications including post-translationalmodifications like phosophorylation or glycosylation. Surface plasmonresonance can be used for quantification of bound protein targets wherethe scaffold-binder(s) are immobilized on a suitable gold-surface (forexample, as obtained from Biacore, Sweden).

Described below are exemplary schemes for selecting binders (in thiscase, Fn-binders specific for the protein, TNF-α) and the use of thoseselected populations for detection on chips. This example is providedfor the purpose of illustrating the invention, and should not beconstrued as limiting.

Selection of TNF-α Binders Based on ¹⁰Fn3 Scaffold

In one exemplary use for scaffold selection on chips, an ¹⁰Fn3-basedselection was performed against TNF-α, using a library of human ¹⁰Fn3variants with randomized loops BC, DE, and FG. The library wasconstructed from three DNA fragments, each of which contained nucleotidesequences that encoded approximately one third of human ¹⁰Fn3, includingone of the randomized loops. The DNA sequences that encoded the loopresidues listed above were rebuilt by oligonucleotide synthesis, so thatthe codons for the residues of interest were replaced by (NNS)_(n),where N represents any of the four deoxyribonucleotides (A, C, G, or T),and S represents either C or G. The C-terminus of each fragmentcontained the sequence for the FLAG purification tag.

Once extended by Klenow, each DNA fragment was transcribed, ligated to apuromycin-containing DNA linker, and translated in vitro, as describedby Szostak et al. (Roberts and Szostak, Proc. Natl. Acad. Sci USA94:12297, 1997; Szostak et al., U.S. Ser. No. 09/007,005 and U.S. Ser.No. 09/247,190; Szostak et al., WO98/31700), to generate an mRNA-peptidefusion, which was then reverse-transcribed into a DNA-mRNA-peptidefusion. The binding of the FLAG-tagged peptide to M2 agarose separatedfull-length fusion molecules from those containing frameshifts orsuperfluous stop codons; the DNA associated with the purifiedfull-length fusion was amplified by PCR, then the three DNA fragmentswere cut by Ear I restriction endonuclease and ligated to form the fulllength template. The template was transcribed, ligated topuromycin-containing DNA linkers, and translated to generate a¹⁰Fn3-RNA/cDNA library, which was then reverse-transcribed to yield theDNA-mRNA-peptide fusion library which was subsequently used in theselection.

Selection for TNF-α binders took place in 50 mM HEPES, pH 7.4, 0.02%Triton-X, 0.1 mg/mL salmon sperm DNA. The PROfusion™ library wasincubated with Sepharose-immobilized TNF-α; after washing, the DNAassociated with the tightest binders was eluted with 0.1 M KOH,amplified by PCR, and transcribed, ligated, translated, andreverse-transcribed into the starting material for the next round ofselection.

Ten rounds of such selection were performed (as shown in FIG. 13); theyresulted in a PROfusion™ pool that bound to TNF-α-Sepharose with theapparent average K_(d) of 120 nM. Specific clonal components of the poolthat were characterized showed TNF-α binding in the range of 50-500 nM.

Immobilization, Target Protein Capture, and MALDI-TOF Detection

As a first step toward immobilizing Fn3 fusions to a chip surface, anoligonucleotide capture probe was prepared with an automated DNAsynthesizer (PE BioSystems Expedite 8909) using the solid-supportphosphoramidite approach. All reagents were obtained from Glen Research.Synthesis was initiated with a solid support containing a disulfide bondto eventually provide a 3′-terminal thiol functionality. The first fourmonomers to be added were hexaethylene oxide units, followed by 20 Tmonomers. The 5′-terminal DMT group was not removed. The capture probewas cleaved from the solid support and deprotected with ammoniumhydroxide, concentrated to dryness in a vacuum centrifuge, and purifiedby reverse-phase HPLC using an acetonitrile gradient in triethylammoniumacetate buffer. Appropriate fractions from the HPLC were collected,evaporated to dryness in a vacuum centrifuge, and the 5′-terminal DMTgroup was removed by treatment with 80% AcOH for 30 minutes. The acidwas removed by evaporation, and the oligonucleotide was then treatedwith 100 mM DTT for 30 minutes to cleave the disulfide bond. DTT wasremoved by repeated extraction with EtOAc. The oligonucleotide wasethanol precipitated from the remaining aqueous layer and checked forpurity by reverse-phase HPLC.

The 3′-thiol capture probe was adjusted to 250 μM in degassed 1×PBSbuffer and applied as a single droplet (75 μL) to a 9×9 mm gold-coatedchip (Biacore) in an argon-flushed chamber containing a small amount ofwater. After 18 hours at room temperature, the capture probe solutionwas removed, and the functionalized chip was washed with 50 mL 1×PBSbuffer (2× for 15 minutes each) with gentle agitation, and then rinsedwith 50 mL water (2× for 15 minutes each) in the same fashion. Remainingliquid was carefully removed and the functionalized chips were eitherused immediately or stored at 4° C. under argon.

About 1 pmol of ¹⁰Fn3 fusion pool from the Round 10 TNF-α selection(above) was treated with RNAse A for several hours, adjusted to 5×SSC in70 μL, and applied to a functionalized gold chip from above as a singledroplet. A 50 μL volume gasket device was used to seal the fusionmixture with the functionalized chip, and the apparatus was continuouslyrotated at 4° C. After 18 hours the apparatus was disassembled, and thegold chip was washed with 50 mL 5×SSC for 10 minutes with gentleagitation. Excess liquid was carefully removed from the chip surface,and the chip was passivated with a blocking solution (1×TBS+0.02%Tween-20+0.25% BSA) for 10 minutes at 4° C. Excess liquid was carefullyremoved, and a solution containing 500 μg/mL TNF-α in the samecomposition blocking solution was applied to the chip as a singledroplet and incubated at 4° C. for two hours with occasional mixing ofthe droplet via Pipetman. After removal of the binding solution, thechip was washed for 5 minutes at 4° C. with gentle agitation (50 mL1×TBS+0.02% Tween-20) and then dried at room temperature. A second chipwas prepared exactly as described above, except fusion was not added tothe hybridization mix.

Next, MALDI-TOF matrix (15 mg/mL 3,5-dimethoxy-4-hydroxycinnamic acid in1:1 ethanol/10% formic acid in water) was uniformly applied to the goldchips with a high-precision 3-axis robot (MicroGrid, BioRobotics). A16-pin tool was used to transfer the matrix from a 384-well microtiterplate to the chips, producing 200 micron diameter features with a 600micron pitch. The MALDI-TOF mass spectrometer (Voyager DE, PerSeptiveBiosystems) instrument settings were as follows: Accelerating Voltage=25k, Grid Voltage=92%, Guide Wire Voltage=0.05%, Delay=200 on, LaserPower=2400, Low Mass Gate=1500, Negative Ions=off. The gold chips wereindividually placed on a MALDI sample stage modified to keep the levelof the chip the same as the level of the stage, thus allowing properflight distance. The instrument's video monitor and motion controlsystem were used to direct the laser beam to individual matrix features.

FIGS. 14 and 15 show the mass spectra from the ¹⁰Fn3 fusion chip and thenon-fusion chip, respectively. In each case, a small number of 200micron features were analyzed to collect the spectra, but FIG. 15required significantly more acquisitions. The signal at 17.4 kDacorresponds to TNF-α monomer.

Immobilization. Target Protein Capture, and Fluorescence Detection

Pre-cleaned 1×3 inch glass microscope slides (Goldseal, #3010) weretreated with Nanostrip (Cyantek) for 15 minutes, 10% aqueous NaOH at 70°C. for 3 minutes, and 1% aqueous HCl for 1 minute, thoroughly rinsingwith deionized water after each reagent. The slides were then dried in avacuum desiccator over anhydrous calcium sulfate for several hours. A 1%solution of aminopropytrimethoxysilane in 95% acetone/5% water wasprepared and allowed to hydrolyze for 20 minutes. The glass slides wereimmersed in the hydrolyzed silane solution for 5 minutes with gentleagitation. Excess silane was removed by subjecting the slides to ten5-minute washes, using fresh portions of 95% acetone/5% water for eachwash, with gentle agitation. The slides were then cured by heating at110° C. for 20 minutes. The silane treated slides were immersed in afreshly prepared 0.2% solution of phenylene 1,4-diisothiocyanate in 90%DMF/10% pyridine for two hours, with gentle agitation. The slides werewashed sequentially with 90% DMF/10% pyridine, methanol, and acetone.After air drying, the functionalized slides were stored at 0° C. in avacuum desiccator over anhydrous calcium sulfate. Similar results wereobtained with commercial amine-reactive slides (3-D Link, Surmodics).

Oligonucleotide capture probes were prepared with an automated DNAsynthesizer (PE BioSystems Expedite 8909) using conventionalphosphoramidite chemistry. All reagents were from Glen Research.Synthesis was initiated with a solid support bearing an orthogonallyprotected amino functionality, whereby the 3′-terminal amine is notunmasked until final deprotection step. The first four monomers to beadded were hexaethylene oxide units, followed by the standard A, G, Cand T monomers. All capture oligo sequences were cleaved from the solidsupport and deprotected with ammonium hydroxide, concentrated todryness, precipitated in ethanol, and purified by reverse-phase HPLCusing an acetonitrile gradient in triethylammonium acetate buffer.Appropriate fractions from the HPLC were collected, evaporated todryness in a vacuum centrifuge, and then coevaporated with a portion ofwater.

The purified, amine-labeled capture oligos were adjusted to aconcentration of 250 μM in 50 mM sodium carbonate buffer (pH 9.0)containing 10% glycerol. The probes were spotted onto the amine-reactiveglass surface at defined positions in a 5×5×6 array pattern with a3-axis robot (MicroGrid, BioRobotics). A 16-pin tool was used totransfer the liquid from 384-well microtiter plates, producing 200micron features with a 600 micron pitch. Each sub-grid of 24 featuresrepresents a single capture probe (i.e., 24 duplicate spots). The arrayswere incubated at room temperature in a moisture-saturated environmentfor 12-18 hours. The attachment reaction was terminated by immersing thechips in 2% aqueous ammonium hydroxide for five minutes with gentleagitation, followed by rinsing with distilled water (3× for 5 minuteseach). The array was finally soaked in 10×PBS solution for 30 minutes atroom temperature, and then rinsed again for 5 minutes in distilledwater.

Specific and thermodynamically isoenergetic sequences along the ¹⁰Fn3mRNA were identified to serve as capture points to self-assemble andanchor the ¹⁰Fn3 protein. The software program HybSimulator v4.0(Advanced Gene Computing Technology, Inc.) facilitated theidentification and analysis of potential capture probes. Six uniquecapture probes were chosen and printed onto the chip, three of which arecomplementary to common regions of the ¹⁰Fn3 fusion pool's mRNA (CP3′,CP5′, and CPflag). The remaining three sequences (CPneg1, CPneg2, andCPneg3) are not complementary and function in part as negative controls.Each of the capture probes possesses a 3′-amino terminus and fourhexaethylene oxide spacer units, as described above. The following is alist of the capture probe sequences that were employed (5′→3′):

CP3′: (SEQ ID NO: 22) TGTAAATAGTAATTGTCCC CP5′: (SEQ ID NO: 23)TTTTTTTTTTTTTTTTTTTT CPneg1:  (SEQ ID NO: 24) CCTGTAGGTGTCCAT CPflag:(SEQ ID NO: 25) CATCGTCCTTGTAGTC CPneg2: (SEQ ID NO: 26) CGTCGTAGGGGTACPneg3:  (SEQ ID NO: 27) CAGGTCTTCTTCAGAGA

About 1 pmol of ¹⁰Fn3 fusion pool from the Round 10 TNF-α selection wasadjusted to 5×SSC containing 0.02% Tween-20 and 2 mM vanadylribonucleotide complex in a total volume of 350 μL. The entire volumewas applied to the microarray under a 400 μL gasket device and theassembly was continuously rotated for 18 hours at room temperature.After hybridization the slide was washed sequentially with stirred 500mL portions of 5×SSC, 2.5×SSC, and 1×SSC for 5 minutes each. Traces ofliquid were removed by centrifugation and the slide was allowed toair-dry.

Recombinant human TNF-α (500 μg, lyophilized, from PreproTech) was takenup in 230 μL 1×PBS and dialyzed against 700 mL stirred 1×PBS at 4° C.for 18 hours in a Microdialyzer unit (3,500 MWCO, Pierce). The dialyzedTNF-α was treated with EZ-Link NHS-LC-LC biotinylation reagent (20 μg,Pierce) for 2 hours at 0° C., and again dialyzed against 700 mL stirred1×PBS at 4° C. for 18 hours in a Microdialyzer unit (3,500 MWCO,Pierce). The resulting conjugate was analyzed by MALDI-TOF massspectrometry and was found to be almost completely functionalized with asingle biotin moiety.

Each of the following processes was conducted at 4° C. with continuousrotation or mixing. The protein microarray surface was passivated bytreatment with 1×TBS containing 0.02% Tween-20 and 0.2% BSA (200 μL) for60 minutes. Biotinylated TNF-α (100 nM concentration made up in thepassivation buffer) was contacted with the microarray for 120 minutes.The microarray was washed with 1×TBS containing 0.02% Tween-20 (3×50 mL,5 minutes each wash). Fluorescently labeled streptavidin (2.5 μg/mLAlexa 546-streptavidin conjugate from Molecular Probes, made up in thepassivation buffer) was contacted with the microarray for 60 minutes.The microarray was washed with 1×TBS containing 0.02% Tween-20 (2×50 mL,5 minutes each wash) followed by a 3 minute rinse with 1×TBS. Traces ofliquid were removed by centrifugation, and the slide was allowed toair-dry at room temperature.

Fluorescence laser scanning was performed with a GSI Lumonics ScanArray5000 system using 10 μM pixel resolution and preset excitation andemission wavelengths for Alexa 546 dye. Phosphorimage analysis wasperformed with a Molecular Dynamics Storm system. Exposure time was 48hours with direct contact between the microarray and the phosphorstorage screen. Phosphorimage scanning was performed at the 50 micronresolution setting, and data was extracted with ImageQuant v.4.3software.

FIGS. 16 and 17 are the phosphorimage and fluorescence scan,respectively, of the same array. The phosphorimage shows where the ¹⁰Fn3fusion hybridized based on the ³⁵S methionine signal. The fluorescencescan shows where the labeled TNF-α bound.

Other Embodiments

Other embodiments are within the claims.

All publications, patents, and patent applications mentioned herein arehereby incorporated by reference.

TABLE 1 A Clone Number BC DE FG Ka (nM) Wt 0 DAPAVTV GSKSGRGDSPASSK >1,000 R0 Pool — XXXXXXX XXXX XXXXXXXXXX >1,000 R09 — XXXXXXXXXXX XXXXXXXXXX  3 ± 2 Pool R10 — XXXXXXX XXXX XXXXXXXXXX  2 ± 1 PoolT09.07 2 ASPPMWC PWAT EYLPEWNMTQ  1 ± 0.5 T10.06 3 NRSGLQS PWASDKSDTYKYDD  2 ± 0.5 T09.12 3 RPTSNPP PWAS AQTGHHLHDK  4 ± 2 T10.15 2HTERSFP PWGS EHYRDTGTGH  4 ± 2 T09.05 2 TTRHSPV PWAT MPTNWRFPHR 17 ± 6T09.03 2 RPNPRLS GLFS PKETSNIFIA 13 ± 6 T10.33 2 SPPNDAH GSKS DQQSYTYYSN17 ± 1 T09.34 2 RTPASPH LLWP PTHMLKPQSM 18 ± 2 T09.14 2 YRHTYRD PWATDTGYDVHTKR 24 ± 2 T09.33 5 NRSGLQS PWAS SNVGRLDTRY PPT

TABLE 2 B Clone Number BC DE FG Ka (nM) Wt 0 DAPAVTV GSKSGRGDSPASSK >1,000 R14 — XXXXXXX XXXX XXXXXXXXXX  0.4 ± 0.2 Pool T14.25 1DTHNAYN HPEV NHHMPLRIFG 0.09 ± 0.02 T14.07 1 RPTSNPP PWAS PVYPMHSMLS0.18 ± 0.02 T14.20 1 RNIYPIA PWAS DKSDTYKYDD 0.11 ± 0.03 T14.24 1NRSGLQC PWAS DQRDTYKYDD 0.32 ± 0.02 T14.22 1 RPGRTYS PWAN FTPGYPLTEM 0.4 ± 0.2 T14.10 1 RPGRTYS PWAN FPPGYPLTEM  0.5 ± 0.2 T14.02 1 MTPHNHVTGNA PHHGHFDLEP  0.5 ± 0.1 T14.06 1 TRTNAST NFWW SPDETSAYSE  1.4 ± 0.4T10.06 8 NRSGLQS PWAS DKSDTYKYDD    2 ± 0.5 T14.21 1 RPGRTYS PWANYTHSTPMQDE    7 ± 2 T09.34 1 RTPASPH LLWP PTHMLKPQSM   18 ± 2 T14.03 1TRTNANT NNPP PDGSRHMLTK >1,000 T14.01 1 DNSRPNT PWGS TSECHKLSST PPTT14.11 1 NPNRSFA PWAS AQTGHHLHDK PPT

TABLE 3 C Clone Number BC DE FG Ka (nM) Wt 0 DAPAVTV GSKSGRGDSPASSK >1,000 M12 — XXXXXXX XXXX XXXXXXXXXX 0.5 Pool M12.04 1SMTPNWP PWAS HRDT 0.02 ± 0.01 T14.25 1 DTHNAYN HPEV IHHMPLRIFG 0.09 ±0.02 M12.18 1 ASPPMW PWAT DESWSDRSMD  0.2 ± 0.1 M12.26 1 RPPADLN PWGTHRDT  0.2 ± 0.1 M12.12 3 EQSPTYG GSKS IEKDRIPLFG  0.2 ± 0.05 M12.13 1RPGRTYS PWAN FPPGYPLTEM  0.3 ± 0.2 M12.16 1 RPGRTYS PWAS DKSGTYRYDD 0.3 ± 0.05 M12.21 1 YRHTYRD PWAT DAGYDVHTKR  0.3 ± 0.1 M12.23 1 RTMPVTAPWAS SATPSRPNVH  0.3 ± 0.1 M12.09 2 RPGRAYS PWAN FPPRYPLTEM  0.4 ± 0.1M12.05 1 SPPNDAH GSKS DQQSYTYYSN  0.5 ± 0.2 M12.08 1 II APKA SHRNHFHVET 0.6 ± 0.05 M12.19 1 RNNQYTP ELNP QNGTPRVIYG  0.6 ± 0.2 M12.22 1 RPASNPAPWAS AQTGHRLHDK  0.7 ± 0.2 M12.24 2 NRSGLQS PWAS PNVGRLDTRY  1.3 ± 0.7M12.01 2 NRSGLQS PWAS DESDTYKYDD  1.6 ± 0.2 M12.14 1 THDNVPA PWASLYTGNHRPEH  1.7 ± 0.4 M12.07 1 RSGNRTT PWAT THNSTAQPEY    4 ± 2 M12.25 1NRSGLQS PWAS SNVGRLDTRY >1000 M12.15 1 RNAKDPG PWGT ATNPGPTQHR PPT

What is claimed is: 1-43. (canceled)
 44. An isolated protein comprisinga domain derived from the tenth module of the human fibronectin type III(¹⁰Fn3) comprising an amino acid sequence that (a) comprises seven betastrands distributed between two antiparallel beta-sheets; (b) comprisesBC, DE and FG loops which connect the beta strands, wherein one, two orthree of said loops are mutated; (c) lacks an integrin binding motif;and (d) is at least 70% identical to the wild-type human ¹⁰Fn3 domain,wherein said derivative ¹⁰Fn3 domain binds with a Kd at least as tightas 1 μM to an antigen.
 45. The protein of claim 44, wherein said proteinis a monomer under physiological conditions.
 46. The protein of claim44, wherein said protein is a dimer under physiological conditions. 47.The protein of claim 44, wherein said protein is fused to a secondprotein domain.
 48. An array comprising a library of proteins comprisinga domain derived from the tenth module of the human fibronectin type III(¹⁰Fn3) comprising an amino acid sequence that (a) comprises seven betastrands distributed between two antiparallel beta-sheets; (b) comprisesBC, DE and FG loops which connect the beta strands, wherein one, two orthree of said loops are mutated; (c) lacks an integrin binding motif;and (d) is at least 70% identical to the wild-type human ¹⁰Fn3 domain.49. A nucleic acid encoding an isolated protein comprising a domainderived from the tenth module of the human fibronectin type III (¹⁰Fn3)comprising an amino acid sequence that (a) comprises seven beta strandsdistributed between two antiparallel beta-sheets; (b) comprises BC, DEand FG loops which connect the beta strands, wherein one, two or threeof said loops are mutated; (c) lacks an integrin binding motif; and (d)is at least 70% identical to the wild-type human ¹⁰Fn3 domain.
 50. Amethod of obtaining a protein comprising a domain derived from the tenthmodule of the wild-type human fibronectin type III (¹⁰Fn3) which bindsto an antigen, the method comprising: (a) providing a wild-type ¹⁰Fn3domain; to t (b) generating mutated derivatives of the wild-type ¹⁰Fn3domain, thereby producing a library of ¹⁰Fn3 domain derivatives; (c)contacting the library with the antigen; (d) selecting from the libraryat least one derivative protein which binds to the antigen with a Kd atleast as tight as 1 μM; and (e) optionally repeating steps (b)-(d). 51.A method of isolating a protein comprising a domain derived from thetenth module of the wild-type human fibronectin type III (¹⁰Fn3) whichbinds to an antigen, the method comprising: (a) contacting the antigenwith a candidate protein comprising a mutated derivative of thewild-type ¹⁰Fn3 domain which binds with a Kd at least as tight as 1 μMthe antigen under conditions that allow antigen-protein complexformation; and (b) obtaining the ¹⁰Fn3 derivative protein from thecomplex.
 52. A method of detecting an antigen in a sample, said methodcomprising: (a) contacting said sample with a protein comprising adomain derived from the tenth module of the wild-type human fibronectintype III (¹⁰Fn3) which binds to the antigen with a Kd at least as tightas 1 μM the antigen under conditions that allow antigen-protein complexformation; and (b) detecting the complex; wherein the detection of thecomplex indicates the presence of the antigen in the sample.
 53. Apharmaceutical composition comprising the protein of claim 44.